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Publications

A generated publication list from PubMed, enriched with Google Scholar citation counts and profile links.

Updated
2026-04-15T18:24:29Z
Publications
187
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184
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26035 citations · h-index 80
This list is generated from PubMed and enriched with citation counts from Google Scholar profile data. Additional profiles: Google Scholar, DiVA, ORCID, and legacy archive.

Publication list

  1. Evaluating deep learning based structure prediction methods on antibody-antigen complexes

    Fromm S, Ludaic M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41863324 · Citations: 8 · Source: pubmed

  2. A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins

    Rosignoli S, Taraglio S, Di Luzio F, Lustrino E, Marzella D, Elofsson A, Panella M, Paiardini A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41712756 · Citations: 0 · Source: pubmed

  3. Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

    Kretsch RC, Posani E, Baulin EF, Bujnicki JM, Bussi G, Cheatham TE 3rd, Chen SJ, Elofsson A, Farsani MA, Fisher ON, Gromiha MM, Gupta A, Hamada M, Harini K, Hu G, Huang D, Iwakiri J, Jain A, Kagaya Y, Kihara D, et al.

    Proteins · Year: 2026 · PMID: 41204761 · Citations: 3 · Source: pubmed

  4. AlphaFold3 at CASP16

    Elofsson A

    Proteins · Year: 2026 · PMID: 40851426 · Citations: 18 · Source: pubmed

  5. Engaging the Community: CASP Special Interest Groups

    Elofsson A, Kretsch RC, Magnus M, Montelione GT

    Proteins · Year: 2026 · PMID: 40304050 · Citations: 3 · Source: pubmed

  6. Blind prediction of complex water and ion ensembles around RNA in CASP16

    Kretsch RC, Posani E, Baulin EF, Bujnicki JM, Bussi G, Cheatham TE 3rd, Chen SJ, Elofsson A, Farsani MA, Fisher ON, Gromiha MM, Gupta A, Hamada M, Harini K, Hu G, Huang D, Iwakiri J, Jain A, Kagaya Y, Kihara D, et al.

    bioRxiv : the preprint server for biology · Year: 2025 · PMID: 41279659 · Citations: 3 · Source: pubmed

  7. Structural host-virus interactome profiling of intact infected cells

    Bogdanow B, Mühlberg L, Gruska I, Vetter B, Ruta J, Elofsson A, Wiebusch L, Liu F

    Nature communications · Year: 2025 · PMID: 40691152 · Citations: 9 · Source: pubmed

  8. Editorial overview: Sequences and topology (2025)

    Elofsson A, Kolodny R

    Current opinion in structural biology · Year: 2025 · PMID: 40602329 · Citations: 0 · Source: pubmed

  9. Unlocking protein networks with Predictomes: The SPOC advantage

    Elofsson A

    Molecular cell · Year: 2025 · PMID: 40118037 · Citations: 0 · Source: pubmed

  10. Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains

    Osterholz H, Stevens A, Abramsson ML, Lama D, Brackmann K, Rising A, Elofsson A, Marklund EG, Deindl S, Leppert A, Landreh M

    JACS Au · Year: 2025 · PMID: 39886581 · Citations: 9 · Source: pubmed

  11. Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies

    Bogdanow B, Ruwolt M, Ruta J, Mühlberg L, Wang C, Zeng WF, Elofsson A, Liu F

    Molecular systems biology · Year: 2025 · PMID: 39653847 · Citations: 2 · Source: pubmed

  12. MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2

    Chim HY, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2024 · PMID: 38781500 · Citations: 13 · Source: pubmed

  13. Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse

    Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L

    eLife · Year: 2024 · PMID: 38666763 · Citations: 34 · Source: pubmed

  14. M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings

    Shenoy A, Kalakoti Y, Sundar D, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2024 · PMID: 38175787 · Citations: 27 · Source: pubmed

  15. Peptide binder design with inverse folding and protein structure prediction

    Bryant P, Elofsson A

    Communications chemistry · Year: 2023 · PMID: 37880344 · Citations: 36 · Source: pubmed

  16. A STRP-ed definition of Structured Tandem Repeats in Proteins

    Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE

    Journal of structural biology · Year: 2023 · PMID: 37652396 · Citations: 13 · Source: pubmed

  17. The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems

    Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Džigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, et al.

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2023 · PMID: 37556498 · Citations: 47 · Source: pubmed

  18. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

    Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 37405868 · Citations: 191 · Source: pubmed

  19. Multiplexed selectivity screening of anti-GPCR antibodies

    Dahl L, Kotliar IB, Bendes A, Dodig-Crnković T, Fromm S, Elofsson A, Uhlén M, Sakmar TP, Schwenk JM

    Science advances · Year: 2023 · PMID: 37134173 · Citations: 23 · Source: pubmed

  20. Progress at protein structure prediction, as seen in CASP15

    Elofsson A

    Current opinion in structural biology · Year: 2023 · PMID: 37060758 · Citations: 119 · Source: pubmed

  21. Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins

    Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P

    BMC biology · Year: 2023 · PMID: 36855050 · Citations: 9 · Source: pubmed

  22. A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1

    Saluri M, Leppert A, Gese GV, Sahin C, Lama D, Kaldmäe M, Chen G, Elofsson A, Allison TM, Arsenian-Henriksson M, Johansson J, Lane DP, Hällberg BM, Landreh M

    PNAS nexus · Year: 2023 · PMID: 36743470 · Citations: 20 · Source: pubmed

  23. AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network

    Kang Y, Elofsson A, Jiang Y, Huang W, Yu M, Li Z

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 36692145 · Citations: 37 · Source: pubmed

  24. Towards a structurally resolved human protein interaction network

    Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A

    Nature structural & molecular biology · Year: 2023 · PMID: 36690744 · Citations: 2 · Source: pubmed

  25. A structural biology community assessment of AlphaFold2 applications

    Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, et al.

    Nature structural & molecular biology · Year: 2022 · PMID: 36344848 · Citations: 712 · Source: pubmed

  26. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

    Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Nature communications · Year: 2022 · PMID: 36224222 · Citations: 0 · Source: pubmed

  27. Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

    Österlund N, Vosselman T, Leppert A, Gräslund A, Jörnvall H, Ilag LL, Marklund EG, Elofsson A, Johansson J, Sahin C, Landreh M

    Molecular & cellular proteomics : MCP · Year: 2022 · PMID: 36115577 · Citations: 10 · Source: pubmed

  28. Complementing machine learning-based structure predictions with native mass spectrometry

    Allison TM, Degiacomi MT, Marklund EG, Jovine L, Elofsson A, Benesch JLP, Landreh M

    Protein science : a publication of the Protein Society · Year: 2022 · PMID: 35634779 · Citations: 21 · Source: pubmed

  29. Author Correction: Improved prediction of protein-protein interactions using AlphaFold2

    Bryant P, Pozzati G, Elofsson A

    Nature communications · Year: 2022 · PMID: 35332153 · Source: pubmed

  30. Improved prediction of protein-protein interactions using AlphaFold2

    Bryant P, Pozzati G, Elofsson A

    Nature communications · Year: 2022 · PMID: 35273146 · Citations: 1162 · Source: pubmed

  31. Scoring of protein-protein docking models utilizing predicted interface residues

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 8 · Source: pubmed

  32. The relationship between ageing and changes in the human blood and brain methylomes

    Bryant P, Elofsson A

    NAR genomics and bioinformatics · Year: 2022 · PMID: 35118376 · Citations: 3 · Source: pubmed

  33. Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion

    Duart G, Lamb J, Ortiz-Mateu J, Elofsson A, Mingarro I

    Journal of molecular biology · Year: 2022 · PMID: 35093395 · Citations: 16 · Source: pubmed

  34. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

    Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, et al.

    Nucleic acids research · Year: 2022 · PMID: 34850135 · Citations: 184 · Source: pubmed

  35. Limits and potential of combined folding and docking

    Pozzati G, Zhu W, Bassot C, Lamb J, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2022 · PMID: 34788800 · Citations: 29 · Source: pubmed

  36. Toward Characterising the Cellular 3D-Proteome

    Elofsson A

    Frontiers in bioinformatics · Year: 2021 · PMID: 36353353 · Citations: 5 · Source: pubmed

  37. Protein sequence-to-structure learning: Is this the end(-to-end revolution)?

    Laine E, Eismann S, Elofsson A, Grudinin S

    Proteins · Year: 2021 · PMID: 34519095 · Citations: 47 · Source: pubmed

  38. The evolutionary history of topological variations in the CPA/AT transporters

    Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 34403419 · Citations: 4 · Source: pubmed

  39. pyconsFold: a fast and easy tool for modeling and docking using distance predictions

    Lamb J, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 34240102 · Citations: 8 · Source: pubmed

  40. GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction

    Li Z, Jiang K, Qin S, Zhong Y, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 34081706 · Citations: 26 · Source: pubmed

  41. Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

    Bassot C, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 33857128 · Citations: 9 · Source: pubmed

  42. GraphQA: protein model quality assessment using graph convolutional networks

    Baldassarre F, Menéndez Hurtado D, Elofsson A, Azizpour H

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 32780838 · Citations: 155 · Source: pubmed

  43. Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries

    Bryant P, Elofsson A

    PeerJ · Year: 2020 · PMID: 32983643 · Citations: 75 · Source: pubmed

  44. Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis

    Naderi R, Saadati Mollaei H, Elofsson A, Hosseini Ashtiani S

    Genes · Year: 2020 · PMID: 32785106 · Citations: 4 · Source: pubmed

  45. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

    Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, et al.

    F1000Research · Year: 2020 · PMID: 32566135 · Citations: 16 · Source: pubmed

  46. Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning

    Bryant P, Elofsson A

    Journal of molecular biology · Year: 2020 · PMID: 32485208 · Citations: 2 · Source: pubmed

  47. Protein Contact Map Prediction Based on ResNet and DenseNet

    Li Z, Lin Y, Elofsson A, Yao Y

    BioMed research international · Year: 2020 · PMID: 32337273 · Citations: 47 · Source: pubmed

  48. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

    Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M

    Genes · Year: 2020 · PMID: 32283633 · Citations: 65 · Source: pubmed

  49. DisProt: intrinsic protein disorder annotation in 2020

    Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, et al.

    Nucleic acids research · Year: 2020 · PMID: 31713636 · Citations: 290 · Source: pubmed

  50. An intrinsically disordered proteins community for ELIXIR

    Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, et al.

    F1000Research · Year: 2019 · PMID: 31824649 · Citations: 19 · Source: pubmed

  51. Detecting sequence signals in targeting peptides using deep learning

    Almagro Armenteros JJ, Salvatore M, Emanuelsson O, Winther O, von Heijne G, Elofsson A, Nielsen H

    Life science alliance · Year: 2019 · PMID: 31570514 · Citations: 1108 · Source: pubmed

  52. Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome b during mitochondrial respiratory chain assembly

    Ndi M, Masuyer G, Dawitz H, Carlström A, Michel M, Elofsson A, Rapp M, Stenmark P, Ott M

    The Journal of biological chemistry · Year: 2019 · PMID: 31537648 · Citations: 12 · Source: pubmed

  53. Why do eukaryotic proteins contain more intrinsically disordered regions?

    Basile W, Salvatore M, Bassot C, Elofsson A

    PLoS computational biology · Year: 2019 · PMID: 31329574 · Citations: 121 · Source: pubmed

  54. Estimation of model accuracy in CASP13

    Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B

    Proteins · Year: 2019 · PMID: 31265154 · Citations: 107 · Source: pubmed

  55. Using PconsC4 and PconsFold2 to Predict Protein Structure

    Bassot C, Menendez Hurtado D, Elofsson A

    Current protocols in bioinformatics · Year: 2019 · PMID: 31063641 · Citations: 7 · Source: pubmed

  56. PconsFam: An Interactive Database of Structure Predictions of Pfam Families

    Lamb J, Jarmolinska AI, Michel M, Menéndez-Hurtado D, Sulkowska JI, Elofsson A

    Journal of molecular biology · Year: 2019 · PMID: 30796988 · Citations: 17 · Source: pubmed

  57. Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

    Elofsson A, Hess B, Lindahl E, Onufriev A, van der Spoel D, Wallqvist A

    PLoS computational biology · Year: 2019 · PMID: 30653494 · Citations: 44 · Source: pubmed

  58. PconsC4: fast, accurate and hassle-free contact predictions

    Michel M, Menéndez Hurtado D, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2019 · PMID: 30590407 · Citations: 107 · Source: pubmed

  59. Improved protein model quality assessments by changing the target function

    Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

    Proteins · Year: 2018 · PMID: 29524250 · Citations: 22 · Source: pubmed

  60. Topology of membrane proteins-predictions, limitations and variations

    Tsirigos KD, Govindarajan S, Bassot C, Västermark Å, Lamb J, Shu N, Elofsson A

    Current opinion in structural biology · Year: 2018 · PMID: 29100082 · Citations: 43 · Source: pubmed

  61. Methods for estimation of model accuracy in CASP12

    Elofsson A, Joo K, Keasar C, Lee J, Maghrabi AHA, Manavalan B, McGuffin LJ, Ménendez Hurtado D, Mirabello C, Pilstål R, Sidi T, Uziela K, Wallner B

    Proteins · Year: 2018 · PMID: 28975666 · Citations: 34 · Source: pubmed

  62. The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction

    Salvatore M, Shu N, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2018 · PMID: 28901589 · Citations: 18 · Source: pubmed

  63. Large-scale structure prediction by improved contact predictions and model quality assessment

    Michel M, Menéndez Hurtado D, Uziela K, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28881974 · Citations: 37 · Source: pubmed

  64. Predicting accurate contacts in thousands of Pfam domain families using PconsC3

    Michel M, Skwark MJ, Menéndez Hurtado D, Ekeberg M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28535189 · Citations: 47 · Source: pubmed

  65. SubCons: a new ensemble method for improved human subcellular localization predictions

    Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28407043 · Citations: 34 · Source: pubmed

  66. High GC content causes orphan proteins to be intrinsically disordered

    Basile W, Sachenkova O, Light S, Elofsson A

    PLoS computational biology · Year: 2017 · PMID: 28355220 · Citations: 82 · Source: pubmed

  67. GWAR: robust analysis and meta-analysis of genome-wide association studies

    Dimou NL, Tsirigos KD, Elofsson A, Bagos PG

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28108451 · Citations: 16 · Source: pubmed

  68. ProQ3D: improved model quality assessments using deep learning

    Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28052925 · Citations: 204 · Source: pubmed

  69. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins

    Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, et al.

    Nucleic acids research · Year: 2017 · PMID: 27965415 · Source: pubmed

  70. DisProt 7.0: a major update of the database of disordered proteins

    Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, et al.

    Nucleic acids research · Year: 2017 · PMID: 27899601 · Citations: 354 · Source: pubmed

  71. ProQ3: Improved model quality assessments using Rosetta energy terms

    Uziela K, Shu N, Wallner B, Elofsson A

    Scientific reports · Year: 2016 · PMID: 27698390 · Citations: 125 · Source: pubmed

  72. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins

    Tsirigos KD, Elofsson A, Bagos PG

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 27587687 · Citations: 96 · Source: pubmed

  73. Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins

    Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 26794316 · Citations: 92 · Source: pubmed

  74. Improved topology prediction using the terminal hydrophobic helices rule

    Peters C, Tsirigos KD, Shu N, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 26644416 · Citations: 66 · Source: pubmed

  75. Molecular architecture of the active mitochondrial protein gate

    Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T

    Science (New York, N.Y.) · Year: 2015 · PMID: 26404837 · Citations: 276 · Source: pubmed

  76. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding

    De Marothy MT, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2015 · PMID: 25970811 · Citations: 59 · Source: pubmed

  77. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

    Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A

    Nucleic acids research · Year: 2015 · PMID: 25969446 · Citations: 1050 · Source: pubmed

  78. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO

    ACS synthetic biology · Year: 2015 · PMID: 25951437 · Citations: 77 · Source: pubmed

  79. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    Hayat S, Sander C, Marks DS, Elofsson A

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2015 · PMID: 25858953 · Citations: 66 · Source: pubmed

  80. Improved contact predictions using the recognition of protein like contact patterns

    Skwark MJ, Raimondi D, Michel M, Elofsson A

    PLoS computational biology · Year: 2014 · PMID: 25375897 · Citations: 190 · Source: pubmed

  81. PconsFold: improved contact predictions improve protein models

    Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2014 · PMID: 25161237 · Citations: 115 · Source: pubmed

  82. Orphans and new gene origination, a structural and evolutionary perspective

    Light S, Basile W, Elofsson A

    Current opinion in structural biology · Year: 2014 · PMID: 24934869 · Citations: 37 · Source: pubmed

  83. The positive inside rule is stronger when followed by a transmembrane helix

    Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A

    Journal of molecular biology · Year: 2014 · PMID: 24927974 · Citations: 19 · Source: pubmed

  84. Large tilts in transmembrane helices can be induced during tertiary structure formation

    Virkki M, Boekel C, Illergård K, Peters C, Shu N, Tsirigos KD, Elofsson A, von Heijne G, Nilsson I

    Journal of molecular biology · Year: 2014 · PMID: 24793448 · Citations: 13 · Source: pubmed

  85. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core

    Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A

    Protein science : a publication of the Protein Society · Year: 2014 · PMID: 24777974 · Citations: 25 · Source: pubmed

  86. Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

    Peters C, Elofsson A

    Proteins · Year: 2014 · PMID: 24753217 · Citations: 31 · Source: pubmed

  87. Protein expansion is primarily due to indels in intrinsically disordered regions

    Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A

    Molecular biology and evolution · Year: 2013 · PMID: 24037790 · Citations: 99 · Source: pubmed

  88. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction

    Skwark MJ, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2013 · PMID: 23677942 · Citations: 34 · Source: pubmed

  89. PconsC: combination of direct information methods and alignments improves contact prediction

    Skwark MJ, Abdel-Rehim A, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2013 · PMID: 23658418 · Citations: 100 · Source: pubmed

  90. The impact of splicing on protein domain architecture

    Light S, Elofsson A

    Current opinion in structural biology · Year: 2013 · PMID: 23562110 · Citations: 54 · Source: pubmed

  91. Membrane protein shaving with thermolysin can be used to evaluate topology predictors

    Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A

    Proteomics · Year: 2013 · PMID: 23512833 · Citations: 15 · Source: pubmed

  92. Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins

    Light S, Sagit R, Ekman D, Elofsson A

    Biochimica et biophysica acta · Year: 2013 · PMID: 23333420 · Citations: 42 · Source: pubmed

  93. Ligand binding properties of human galanin receptors

    Jurkowski W, Yazdi S, Elofsson A

    Molecular membrane biology · Year: 2013 · PMID: 23237663 · Citations: 26 · Source: pubmed

  94. Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion

    Bañó-Polo M, Martínez-Gil L, Wallner B, Nieva JL, Elofsson A, Mingarro I

    Journal of molecular biology · Year: 2013 · PMID: 23228331 · Citations: 42 · Source: pubmed

  95. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins

    Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A, Horton P

    Methods in molecular biology (Clifton, N.J.) · Year: 2013 · PMID: 23192545 · Citations: 6 · Source: pubmed

  96. Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions

    Hayat S, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2012 · PMID: 22689784 · Citations: 14 · Source: pubmed

  97. A guideline to proteome-wide α-helical membrane protein topology predictions

    Tsirigos KD, Hennerdal A, Käll L, Elofsson A

    Proteomics · Year: 2012 · PMID: 22685073 · Citations: 42 · Source: pubmed

  98. The interface of protein structure, protein biophysics, and molecular evolution

    Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, et al.

    Protein science : a publication of the Protein Society · Year: 2012 · PMID: 22528593 · Citations: 258 · Source: pubmed

  99. The evolution of filamin-a protein domain repeat perspective

    Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A

    Journal of structural biology · Year: 2012 · PMID: 22414427 · Citations: 30 · Source: pubmed

  100. BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

    Hayat S, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2012 · PMID: 22247276 · Citations: 100 · Source: pubmed

  101. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

    Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B

    Nature · Year: 2012 · PMID: 22230960 · Citations: 434 · Source: pubmed

  102. Manipulating the genetic code for membrane protein production: what have we learnt so far?

    Nørholm MH, Light S, Virkki MT, Elofsson A, von Heijne G, Daley DO

    Biochimica et biophysica acta · Year: 2012 · PMID: 21884679 · Citations: 44 · Source: pubmed

  103. An introduction to membrane proteins

    Hedin LE, Illergård K, Elofsson A

    Journal of proteome research · Year: 2011 · PMID: 21815691 · Citations: 147 · Source: pubmed

  104. The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity

    Basmarke-Wehelie R, Sjölinder H, Jurkowski W, Elofsson A, Arnqvist A, Engstrand L, Hagner M, Wallin E, Guan N, Kuranasekera H, Aro H, Jonsson AB

    Gastroenterology · Year: 2011 · PMID: 21699774 · Citations: 14 · Source: pubmed

  105. KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2

    Shu N, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21505030 · Citations: 9 · Source: pubmed

  106. Rapid membrane protein topology prediction

    Hennerdal A, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21493661 · Citations: 67 · Source: pubmed

  107. Improved predictions by Pcons.net using multiple templates

    Larsson P, Skwark MJ, Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21149277 · Citations: 19 · Source: pubmed

  108. Why are polar residues within the membrane core evolutionary conserved?

    Illergård K, Kauko A, Elofsson A

    Proteins · Year: 2011 · PMID: 20938980 · Citations: 67 · Source: pubmed

  109. Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants

    Lima Mde F, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PC

    BMC plant biology · Year: 2010 · PMID: 21087491 · Citations: 40 · Source: pubmed

  110. Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare

    Hennerdal A, Falk J, Lindahl E, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2010 · PMID: 20882639 · Citations: 23 · Source: pubmed

  111. Determining receptor-ligand interaction of human galanin receptor type 3

    Runesson J, Sollenberg UE, Jurkowski W, Yazdi S, Eriksson EE, Elofsson A, Langel U

    Neurochemistry international · Year: 2010 · PMID: 20817064 · Citations: 20 · Source: pubmed

  112. Nebulin: a study of protein repeat evolution

    Björklund AK, Light S, Sagit R, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 20643138 · Citations: 58 · Source: pubmed

  113. MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane

    Illergård K, Callegari S, Elofsson A

    BMC bioinformatics · Year: 2010 · PMID: 20565847 · Citations: 44 · Source: pubmed

  114. Repositioning of transmembrane alpha-helices during membrane protein folding

    Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 2010 · PMID: 20109468 · Citations: 88 · Source: pubmed

  115. Identifying and quantifying orphan protein sequences in fungi

    Ekman D, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 19944701 · Citations: 80 · Source: pubmed

  116. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context

    Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch-Bader M, Nilsson I, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 19931281 · Citations: 129 · Source: pubmed

  117. Assessment of global and local model quality in CASP8 using Pcons and ProQ

    Larsson P, Skwark MJ, Wallner B, Elofsson A

    Proteins · Year: 2009 · PMID: 19544566 · Citations: 83 · Source: pubmed

  118. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores

    Illergård K, Ardell DH, Elofsson A

    Proteins · Year: 2009 · PMID: 19507241 · Citations: 696 · Source: pubmed

  119. TOPCONS: consensus prediction of membrane protein topology

    Bernsel A, Viklund H, Hennerdal A, Elofsson A

    Nucleic acids research · Year: 2009 · PMID: 19429891 · Citations: 643 · Source: pubmed

  120. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

    Viklund H, Bernsel A, Skwark M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2008 · PMID: 18945683 · Citations: 287 · Source: pubmed

  121. Quantitative assessment of the structural bias in protein-protein interaction assays

    Björklund AK, Light S, Hedin L, Elofsson A

    Proteomics · Year: 2008 · PMID: 18924110 · Citations: 30 · Source: pubmed

  122. Arrangements in the modular evolution of proteins

    Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A

    Trends in biochemical sciences · Year: 2008 · PMID: 18656364 · Citations: 274 · Source: pubmed

  123. Coils in the membrane core are conserved and functionally important

    Kauko A, Illergård K, Elofsson A

    Journal of molecular biology · Year: 2008 · PMID: 18511074 · Citations: 45 · Source: pubmed

  124. Prediction of membrane-protein topology from first principles

    Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2008 · PMID: 18477697 · Citations: 366 · Source: pubmed

  125. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

    Viklund H, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2008 · PMID: 18474507 · Citations: 482 · Source: pubmed

  126. Using multiple templates to improve quality of homology models in automated homology modeling

    Larsson P, Wallner B, Lindahl E, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2008 · PMID: 18441233 · Citations: 212 · Source: pubmed

  127. Estimating the length of transmembrane helices using Z-coordinate predictions

    Papaloukas C, Granseth E, Viklund H, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2008 · PMID: 18096645 · Citations: 28 · Source: pubmed

  128. Remote homology detection of integral membrane proteins using conserved sequence features

    Bernsel A, Viklund H, Elofsson A

    Proteins · Year: 2008 · PMID: 18076048 · Citations: 14 · Source: pubmed

  129. Prediction of global and local model quality in CASP7 using Pcons and ProQ

    Wallner B, Elofsson A

    Proteins · Year: 2007 · PMID: 17894353 · Citations: 121 · Source: pubmed

  130. Quantification of the elevated rate of domain rearrangements in metazoa

    Ekman D, Björklund AK, Elofsson A

    Journal of molecular biology · Year: 2007 · PMID: 17689563 · Citations: 116 · Source: pubmed

  131. Pcons.net: protein structure prediction meta server

    Wallner B, Larsson P, Elofsson A

    Nucleic acids research · Year: 2007 · PMID: 17584798 · Citations: 78 · Source: pubmed

  132. Membrane protein structure: prediction versus reality

    Elofsson A, von Heijne G

    Annual review of biochemistry · Year: 2007 · PMID: 17579561 · Citations: 329 · Source: pubmed

  133. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

    Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA

    Genome biology · Year: 2007 · PMID: 17521457 · Citations: 53 · Source: pubmed

  134. Expansion of protein domain repeats

    Björklund AK, Ekman D, Elofsson A

    PLoS computational biology · Year: 2006 · PMID: 16933986 · Citations: 306 · Source: pubmed

  135. ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins

    Granseth E, Viklund H, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2006 · PMID: 16873471 · Citations: 65 · Source: pubmed

  136. Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps

    Ohlson T, Aggarwal V, Elofsson A, MacCallum RM

    BMC bioinformatics · Year: 2006 · PMID: 16869963 · Citations: 14 · Source: pubmed

  137. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

    Viklund H, Granseth E, Elofsson A

    Journal of molecular biology · Year: 2006 · PMID: 16860824 · Citations: 115 · Source: pubmed

  138. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

    Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Luigi Martelli P, Casadio R

    Nucleic acids research · Year: 2006 · PMID: 16844984 · Citations: 49 · Source: pubmed

  139. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

    Ekman D, Light S, Björklund AK, Elofsson A

    Genome biology · Year: 2006 · PMID: 16780599 · Citations: 457 · Source: pubmed

  140. Identification of correct regions in protein models using structural, alignment, and consensus information

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2006 · PMID: 16522791 · Citations: 239 · Source: pubmed

  141. Preferential attachment in the evolution of metabolic networks

    Light S, Kraulis P, Elofsson A

    BMC genomics · Year: 2005 · PMID: 16281983 · Citations: 99 · Source: pubmed

  142. ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins

    Ohlson T, Elofsson A

    BMC bioinformatics · Year: 2005 · PMID: 16225676 · Citations: 27 · Source: pubmed

  143. Pcons5: combining consensus, structural evaluation and fold recognition scores

    Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2005 · PMID: 16204344 · Citations: 127 · Source: pubmed

  144. Domain rearrangements in protein evolution

    Björklund AK, Ekman D, Light S, Frey-Skött J, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 16198373 · Citations: 243 · Source: pubmed

  145. Tertiary windowing to detect positive diversifying selection

    Berglund AC, Wallner B, Elofsson A, Liberles DA

    Journal of molecular evolution · Year: 2005 · PMID: 15883884 · Citations: 46 · Source: pubmed

  146. All are not equal: a benchmark of different homology modeling programs

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2005 · PMID: 15840834 · Citations: 299 · Source: pubmed

  147. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions

    Ekman D, Björklund AK, Frey-Skött J, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 15808866 · Citations: 301 · Source: pubmed

  148. A study of the membrane-water interface region of membrane proteins

    Granseth E, von Heijne G, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 15663952 · Citations: 212 · Source: pubmed

  149. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods

    Ohlson T, Wallner B, Elofsson A

    Proteins · Year: 2004 · PMID: 15326603 · Citations: 132 · Source: pubmed

  150. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

    Viklund H, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2004 · PMID: 15215532 · Citations: 318 · Source: pubmed

  151. Using evolutionary information for the query and target improves fold recognition

    Wallner B, Fang H, Ohlson T, Frey-Skött J, Elofsson A

    Proteins · Year: 2004 · PMID: 14696196 · Citations: 47 · Source: pubmed

  152. LiveBench-6: large-scale automated evaluation of protein structure prediction servers

    Rychlewski L, Fischer D, Elofsson A

    Proteins · Year: 2003 · PMID: 14579344 · Citations: 87 · Source: pubmed

  153. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

    Wallner B, Fang H, Elofsson A

    Proteins · Year: 2003 · PMID: 14579343 · Citations: 154 · Source: pubmed

  154. CAFASP3: the third critical assessment of fully automated structure prediction methods

    Fischer D, Rychlewski L, Dunbrack RL Jr, Ortiz AR, Elofsson A

    Proteins · Year: 2003 · PMID: 14579340 · Citations: 153 · Source: pubmed

  155. In silico prediction of the peroxisomal proteome in fungi, plants and animals

    Emanuelsson O, Elofsson A, von Heijne G, Cristóbal S

    Journal of molecular biology · Year: 2003 · PMID: 12823981 · Citations: 128 · Source: pubmed

  156. 3D-Jury: a simple approach to improve protein structure predictions

    Ginalski K, Elofsson A, Fischer D, Rychlewski L

    Bioinformatics (Oxford, England) · Year: 2003 · PMID: 12761065 · Citations: 921 · Source: pubmed

  157. Can correct protein models be identified?

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2003 · PMID: 12717029 · Citations: 863 · Source: pubmed

  158. Prediction of MHC class I binding peptides, using SVMHC

    Dönnes P, Elofsson A

    BMC bioinformatics · Year: 2002 · PMID: 12225620 · Citations: 369 · Source: pubmed

  159. The salmon genome (and other issues in bioinformatics)

    Milchert LE, Liberles DA, Elofsson A

    Genome biology · Year: 2002 · PMID: 12184805 · Citations: 4 · Source: pubmed

  160. Improved detection of homologous membrane proteins by inclusion of information from topology predictions

    Hedman M, Deloof H, Von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2002 · PMID: 11847287 · Citations: 31 · Source: pubmed

  161. A study on protein sequence alignment quality

    Elofsson A

    Proteins · Year: 2002 · PMID: 11835508 · Citations: 96 · Source: pubmed

  162. LiveBench-2: large-scale automated evaluation of protein structure prediction servers

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Proteins · Year: 2001 · PMID: 11835496 · Citations: 101 · Source: pubmed

  163. CAFASP2: the second critical assessment of fully automated structure prediction methods

    Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL Jr

    Proteins · Year: 2001 · PMID: 11835495 · Citations: 136 · Source: pubmed

  164. Pcons: a neural-network-based consensus predictor that improves fold recognition

    Lundström J, Rychlewski L, Bujnicki J, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2001 · PMID: 11604541 · Citations: 385 · Source: pubmed

  165. A study of quality measures for protein threading models

    Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A

    BMC bioinformatics · Year: 2001 · PMID: 11545673 · Citations: 281 · Source: pubmed

  166. Structure prediction meta server

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Bioinformatics (Oxford, England) · Year: 2001 · PMID: 11524381 · Citations: 259 · Source: pubmed

  167. LiveBench-1: continuous benchmarking of protein structure prediction servers

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Protein science : a publication of the Protein Society · Year: 2001 · PMID: 11266621 · Citations: 141 · Source: pubmed

  168. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2

    Fischer D, Elofsson A, Rychlewski L

    Protein engineering · Year: 2000 · PMID: 11112504 · Citations: 24 · Source: pubmed

  169. MaxSub: an automated measure for the assessment of protein structure prediction quality

    Siew N, Elofsson A, Rychlewski L, Fischer D

    Bioinformatics (Oxford, England) · Year: 2000 · PMID: 11108700 · Citations: 490 · Source: pubmed

  170. Identification of related proteins on family, superfamily and fold level

    Lindahl E, Elofsson A

    Journal of molecular biology · Year: 2000 · PMID: 10623551 · Citations: 257 · Source: pubmed

  171. Study of the electrostatics treatment in molecular dynamics simulations

    Garemyr R, Elofsson A

    Proteins · Year: 1999 · PMID: 10591101 · Citations: 36 · Source: pubmed

  172. Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale

    Monné M, Nilsson I, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 1999 · PMID: 10543969 · Citations: 117 · Source: pubmed

  173. CAFASP-1: critical assessment of fully automated structure prediction methods

    Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M

    Proteins · Year: 1999 · PMID: 10526371 · Citations: 234 · Source: pubmed

  174. A comparison of sequence and structure protein domain families as a basis for structural genomics

    Elofsson A, Sonnhammer EL

    Bioinformatics (Oxford, England) · Year: 1999 · PMID: 10383473 · Citations: 91 · Source: pubmed

  175. Hidden Markov models that use predicted secondary structures for fold recognition

    Hargbo J, Elofsson A

    Proteins · Year: 1999 · PMID: 10373007 · Citations: 113 · Source: pubmed

  176. Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70

    Zhang XP, Elofsson A, Andreu D, Glaser E

    Journal of molecular biology · Year: 1999 · PMID: 10329135 · Citations: 30 · Source: pubmed

  177. Architecture of beta-barrel membrane proteins: analysis of trimeric porins

    Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 1998 · PMID: 9761484 · Citations: 67 · Source: pubmed

  178. Helix-helix packing in a membrane-like environment

    Mingarro I, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 1997 · PMID: 9325117 · Citations: 46 · Source: pubmed

  179. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method

    Cserzö M, Wallin E, Simon I, von Heijne G, Elofsson A

    Protein engineering · Year: 1997 · PMID: 9278280 · Citations: 1385 · Source: pubmed

  180. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria

    Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 1997 · PMID: 9098890 · Citations: 193 · Source: pubmed

  181. Assessing the performance of fold recognition methods by means of a comprehensive benchmark

    Fischer D, Elofsson A, Rice D, Eisenberg D

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · Year: 1996 · PMID: 9390240 · Citations: 191 · Source: pubmed

  182. A study of combined structure/sequence profiles

    Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D

    Folding & design · Year: 1996 · PMID: 9080191 · Citations: 72 · Source: pubmed

  183. Local moves: an efficient algorithm for simulation of protein folding

    Elofsson A, Le Grand SM, Eisenberg D

    Proteins · Year: 1995 · PMID: 8539252 · Citations: 87 · Source: pubmed

  184. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin

    Elofsson A, Nilsson L

    Journal of molecular biology · Year: 1993 · PMID: 8411178 · Citations: 106 · Source: pubmed

  185. Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

    Elofsson A, Kulinski T, Rigler R, Nilsson L

    Proteins · Year: 1993 · PMID: 8265564 · Citations: 10 · Source: pubmed

  186. Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia coli thioredoxin studied by site-directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamics simulations

    Elofsson A, Rigler R, Nilsson L, Roslund J, Krause G, Holmgren A

    Biochemistry · Year: 1991 · PMID: 1911751 · Source: pubmed

  187. Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations

    Elofsson A, Nilsson L, Rigler R

    International journal of peptide and protein research · Year: 1990 · PMID: 1980672 · Citations: 5 · Source: pubmed

Query: "Kundrotas P" | Publications: 74 | Citation matches: 6

  1. Dockground: Expanding the Resource to Protein-DNA Complexes

    Collins KW, Copeland MM, Kundrotas PJ, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 41274550

  2. Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking

    Singh A, Copeland MM, Kundrotas PJ, Vakser IA

    Proteins · Year: 2025 · PMID: 40476317

  3. GRAMMCell: Docking-based Cell Modeling Resource

    Singh A, Tytarenko AM, Ambati VK, Copeland MM, Kundrotas PJ, Kasyanov PO, Feinberg EA, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 40133778

  4. Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment

    Tytarenko AM, Singh A, Ambati VK, Copeland MM, Kundrotas PJ, Halfmann R, Kasyanov PO, Feinberg EA, Vakser IA

    The journal of physical chemistry. B · Year: 2025 · PMID: 40077832

  5. Dockground: The Resource Expands to Protein-RNA Interactome

    Collins KW, Copeland MM, Kundrotas PJ, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 39956358

  6. CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes

    Collins KW, Copeland MM, Brysbaert G, Wodak SJ, Bonvin AMJJ, Kundrotas PJ, Vakser IA, Lensink MF

    Journal of molecular biology · Year: 2024 · PMID: 39237205

  7. Diffusion of proteins in crowded solutions studied by docking-based modeling

    Singh A, Kundrotas PJ, Vakser IA

    The Journal of chemical physics · Year: 2024 · PMID: 39225532

  8. GRAMM Web Server for Protein Docking

    Singh A, Copeland MM, Kundrotas PJ, Vakser IA

    Methods in molecular biology (Clifton, N.J.) · Year: 2024 · PMID: 37676594

  9. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

    Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 37405868 · Citations: 191

  10. Editorial: Protein recognition and associated diseases

    Gromiha MM, Kundrotas P, Marti MA, Venclovas Č, Li M

    Frontiers in bioinformatics · Year: 2023 · PMID: 37283696

  11. Towards a structurally resolved human protein interaction network

    Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A

    Nature structural & molecular biology · Year: 2023 · PMID: 36690744 · Citations: 2

  12. Size of the protein-protein energy funnel in crowded environment

    Jenkins NW, Kundrotas PJ, Vakser IA

    Frontiers in molecular biosciences · Year: 2022 · PMID: 36425657

  13. A structural biology community assessment of AlphaFold2 applications

    Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, et al.

    Nature structural & molecular biology · Year: 2022 · PMID: 36344848 · Citations: 712

  14. Dockground resource for protein recognition studies

    Collins KW, Copeland MM, Kotthoff I, Singh A, Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2022 · PMID: 36281025

  15. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

    Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Nature communications · Year: 2022 · PMID: 36224222 · Citations: 0

  16. Docking-based long timescale simulation of cell-size protein systems at atomic resolution

    Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2022 · PMID: 36191203

  17. GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes

    Malladi S, Powell HR, David A, Islam SA, Copeland MM, Kundrotas PJ, Sternberg MJE, Vakser IA

    Journal of molecular biology · Year: 2022 · PMID: 35662458

  18. DOCKGROUND membrane protein-protein set

    Kotthoff I, Kundrotas PJ, Vakser IA

    PloS one · Year: 2022 · PMID: 35580077

  19. Scoring of protein-protein docking models utilizing predicted interface residues

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 8

  20. Dockground scoring benchmarks for protein docking

    Kotthoff I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2022 · PMID: 35072956

  21. Limits and potential of combined folding and docking

    Pozzati G, Zhu W, Bassot C, Lamb J, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2022 · PMID: 34788800 · Citations: 29

  22. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

    Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, et al.

    Proteins · Year: 2021 · PMID: 34453465

  23. Structural motifs in protein cores and at protein-protein interfaces are different

    Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2021 · PMID: 33166001

  24. Text mining for modeling of protein complexes enhanced by machine learning

    Badal VD, Kundrotas PJ, Vakser IA

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 32960948

  25. Dockground Tool for Development and Benchmarking of Protein Docking Procedures

    Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA

    Methods in molecular biology (Clifton, N.J.) · Year: 2020 · PMID: 32621232

  26. Application of docking methodologies to modeled proteins

    Singh A, Dauzhenka T, Kundrotas PJ, Sternberg MJE, Vakser IA

    Proteins · Year: 2020 · PMID: 32170770

  27. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

    Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA

    Proteins · Year: 2020 · PMID: 31994759

  28. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

    Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, et al.

    Proteins · Year: 2019 · PMID: 31612567

  29. Gene ontology improves template selection in comparative protein docking

    Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA

    Proteins · Year: 2019 · PMID: 30520123

  30. Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking

    Dauzhenka T, Kundrotas PJ, Vakser IA

    Journal of computational chemistry · Year: 2018 · PMID: 30226647

  31. Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

    Anishchenko I, Kundrotas PJ, Vakser IA

    Biophysical journal · Year: 2018 · PMID: 30122295

  32. Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

    Belkin S, Kundrotas PJ, Vakser IA

    Journal of computer-aided molecular design · Year: 2018 · PMID: 30003468

  33. Natural language processing in text mining for structural modeling of protein complexes

    Badal VD, Kundrotas PJ, Vakser IA

    BMC bioinformatics · Year: 2018 · PMID: 29506465

  34. Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

    Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA

    Proteins · Year: 2018 · PMID: 28905425

  35. Dockground: A comprehensive data resource for modeling of protein complexes

    Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2018 · PMID: 28891124

  36. Structural quality of unrefined models in protein docking

    Anishchenko I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2017 · PMID: 27756103

  37. Modeling complexes of modeled proteins

    Anishchenko I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2017 · PMID: 27701777

  38. Template-Based Modeling of Protein-RNA Interactions

    Zheng J, Kundrotas PJ, Vakser IA, Liu S

    PLoS computational biology · Year: 2016 · PMID: 27662342

  39. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

    Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, et al.

    Proteins · Year: 2016 · PMID: 27122118

  40. Text Mining for Protein Docking

    Badal VD, Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2015 · PMID: 26650466

  41. Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource

    Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA

    BMC bioinformatics · Year: 2015 · PMID: 26227548

  42. Protein models docking benchmark 2

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2015 · PMID: 25712716

  43. Structural templates for comparative protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2015 · PMID: 25488330

  44. Blind prediction of interfacial water positions in CAPRI

    Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, et al.

    Proteins · Year: 2014 · PMID: 24155158

  45. Protein models: the Grand Challenge of protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2014 · PMID: 23934791

  46. Structural templates for modeling homodimers

    Kundrotas PJ, Vakser IA, Janin J

    Protein science : a publication of the Protein Society · Year: 2013 · PMID: 23996787

  47. Global and local structural similarity in protein-protein complexes: implications for template-based docking

    Kundrotas PJ, Vakser IA

    Proteins · Year: 2013 · PMID: 23946125

  48. Protein-protein alternative binding modes do not overlap

    Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2013 · PMID: 23775945

  49. GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

    Kundrotas PJ, Zhu Z, Vakser IA

    Human genomics · Year: 2012 · PMID: 23245398

  50. Templates are available to model nearly all complexes of structurally characterized proteins

    Kundrotas PJ, Zhu Z, Janin J, Vakser IA

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2012 · PMID: 22645367

  51. Protein docking by the interface structure similarity: how much structure is needed?

    Sinha R, Kundrotas PJ, Vakser IA

    PloS one · Year: 2012 · PMID: 22348074

  52. Docking by structural similarity at protein-protein interfaces

    Sinha R, Kundrotas PJ, Vakser IA

    Proteins · Year: 2010 · PMID: 20715056

  53. Accuracy of protein-protein binding sites in high-throughput template-based modeling

    Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2010 · PMID: 20369011

  54. GWIDD: Genome-wide protein docking database

    Kundrotas PJ, Zhu Z, Vakser IA

    Nucleic acids research · Year: 2010 · PMID: 19900970

  55. On the electrostatic component of protein-protein binding free energy

    Talley K, Ng C, Shoppell M, Kundrotas P, Alexov E

    PMC biophysics · Year: 2008 · PMID: 19351424

  56. Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles

    Kundrotas PJ, Lensink MF, Alexov E

    International journal of biological macromolecules · Year: 2008 · PMID: 18572239

  57. Predicting 3D structures of protein-protein complexes

    Vakser IA, Kundrotas P

    Current pharmaceutical biotechnology · Year: 2008 · PMID: 18393862

  58. Predicting interacting and interfacial residues using continuous sequence segments

    Kundrotas P, Alexov E

    International journal of biological macromolecules · Year: 2007 · PMID: 17850859

  59. Optimization of electrostatic interactions in protein-protein complexes

    Brock K, Talley K, Coley K, Kundrotas P, Alexov E

    Biophysical journal · Year: 2007 · PMID: 17693468

  60. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families

    Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E

    Journal of bioinformatics and computational biology · Year: 2007 · PMID: 17688312

  61. BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families

    Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E

    International journal of biological macromolecules · Year: 2007 · PMID: 17320167

  62. PROTCOM: searchable database of protein complexes enhanced with domain-domain structures

    Kundrotas PJ, Alexov E

    Nucleic acids research · Year: 2007 · PMID: 17071962

  63. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

    Kundrotas PJ, Alexov EG

    BMC bioinformatics · Year: 2006 · PMID: 17109752

  64. Predicting 3D structures of transient protein-protein complexes by homology

    Kundrotas PJ, Alexov E

    Biochimica et biophysica acta · Year: 2006 · PMID: 16963323

  65. Electrostatic properties of protein-protein complexes

    Kundrotas PJ, Alexov E

    Biophysical journal · Year: 2006 · PMID: 16782791

  66. Statistical studies of flexible nonhomogeneous polypeptide chains

    Kundrotas PJ

    Biomacromolecules · Year: 2005 · PMID: 16283721

  67. Charge sequence coding in statistical modeling of unfolded proteins

    Kundrotas PJ, Karshikoff A

    Biochimica et biophysica acta · Year: 2004 · PMID: 15450845

  68. Computation of the Ising partition function for two-dimensional square grids

    Häggkvist R, Rosengren A, Andrén D, Kundrotas P, Lundow PH, Markström K

    Physical review. E, Statistical, nonlinear, and soft matter physics · Year: 2004 · PMID: 15169066

  69. Modeling of denatured state for calculation of the electrostatic contribution to protein stability

    Kundrotas PJ, Karshikoff A

    Protein science : a publication of the Protein Society · Year: 2002 · PMID: 12070320

  70. Model for calculation of electrostatic interactions in unfolded proteins

    Kundrotas PJ, Karshikoff A

    Physical review. E, Statistical, nonlinear, and soft matter physics · Year: 2002 · PMID: 11800712

  71. Dynamics of oxygen ordering in the cell-doubled phase of YBa2Cu3O6+x

    Kundrotas PJ, Tornau EE, Rosengren A

    Physical review. B, Condensed matter · Year: 1996 · PMID: 9986342

  72. Phase transitions in the three-state antiferromagnetic Potts model

    Kundrotas PJ, Lapinskas S, Rosengren A

    Physical review. B, Condensed matter · Year: 1995 · PMID: 9979951

  73. Oxygen ordering and states of holes in YBa2Cu3O6+x

    Zubkus VE, Vujicic GM, Kundrotas PJ, Tatarskij VV

    Physical review. B, Condensed matter · Year: 1992 · PMID: 10000978

  74. Phase diagrams of oxygen ordering in high-temperature superconductors RBa2Cu3O7-x

    Zubkus VE, Tornau EE, Lapinskas S, Kundrotas PJ

    Physical review. B, Condensed matter · Year: 1991 · PMID: 9997133

Query: "Narrowe Danielsson S"[Author] OR "Narrowe S"[Author] | Publications: 0 | Citation matches: 0

    Query: "Viliuga V"[Author] | Publications: 1 | Citation matches: 0

    1. ColBuilder: flexible structure generation of crosslinked collagen fibrils

      Monego D, Brosz M, Buck J, Viliuga V, Greicius P, Jung J, Stuehn T, Schmies M, Sugita Y, Gräter F

      Bioinformatics (Oxford, England) · Year: 2025 · PMID: 40323309

    Query: "Ludaic M"[Author] | Publications: 1 | Citation matches: 1

    1. Evaluating deep learning based structure prediction methods on antibody-antigen complexes

      Fromm S, Ludaic M, Elofsson A

      Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41863324 · Citations: 8

    Query: "Matteo Tadiello"[Author] | Publications: 0 | Citation matches: 0

      Query: "Oswal, Anu"[Author] | Publications: 1 | Citation matches: 0

      1. MAVISp: A modular structure-based framework for protein variant effects

        Arnaudi M, Utichi M, Degn K, Tiberti M, Beltrame L, Krzesińska K, Besora PS, Kiachaki E, Scrima S, Bauer L, Meldgård K, Melidi A, Favaro L, Oswal A, Tedeschi G, Dorčaková T, Estad AH, Breitenstein J, Safer J, Saridaki P, et al.

        Protein science : a publication of the Protein Society · Year: 2026 · PMID: 41944585

      Query: "Panconi L"[Author] | Publications: 5 | Citation matches: 0

      1. Mapping membrane biophysical nano-environments

        Panconi L, Euchner J, Tashev SA, Makarova M, Herten DP, Owen DM, Nieves DJ

        Nature communications · Year: 2024 · PMID: 39511199

      2. Three-dimensional topology-based analysis segments volumetric and spatiotemporal fluorescence microscopy

        Panconi L, Tansell A, Collins AJ, Makarova M, Owen DM

        Biological imaging · Year: 2023 · PMID: 38516632

      3. Cluster analysis for localisation-based data sets: dos and don'ts when quantifying protein aggregates

        Panconi L, Owen DM, Griffié J

        Frontiers in bioinformatics · Year: 2023 · PMID: 38076028

      4. Phospholipid tail asymmetry allows cellular adaptation to anoxic environments

        Panconi L, Lorenz CD, May RC, Owen DM, Makarova M

        The Journal of biological chemistry · Year: 2023 · PMID: 37562570

      5. Topology-based fluorescence image analysis for automated cell identification and segmentation

        Panconi L, Makarova M, Lambert ER, May RC, Owen DM

        Journal of biophotonics · Year: 2023 · PMID: 36349740

      Query: "Cucchi, Ivan"[Author] | Publications: 3 | Citation matches: 0

      1. MOLECULE: Molecular-dynamics and Optimized deep Learning for Entropy-regularized Classification and Uncertainty-aware Ligand Evaluation

        Cucchi I, Frasnetti E, Frigerio F, Cinquini F, Pavoni S, Pavarino LF, Colombo G

        Journal of chemical theory and computation · Year: 2025 · PMID: 40931675

      2. Large-scale energy decomposition for the analysis of protein stability

        Mansoor S, Frasnetti E, Cucchi I, Magni A, Bonollo G, Serapian SA, Pavarino LF, Colombo G

        Cell stress & chaperones · Year: 2025 · PMID: 39884551

      3. Integrating Molecular Dynamics and Machine Learning Algorithms to Predict the Functional Profile of Kinase Ligands

        Frasnetti E, Cucchi I, Pavoni S, Frigerio F, Cinquini F, Serapian SA, Pavarino LF, Colombo G

        Journal of chemical theory and computation · Year: 2024 · PMID: 39387368