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Iain H. Moal - Publications

Affiliations: 
2011-2015 Barcelona Supercomputing Center, Barcelona, Catalunya, Spain 
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Moal IH, Chaleil RAG, Torchala M, Bates PA. A Guide for Protein-Protein Docking Using SwarmDock. Methods in Molecular Biology (Clifton, N.J.). 2165: 199-216. PMID 32621226 DOI: 10.1007/978-1-0716-0708-4_11  0.479
2019 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, ... ... Moal IH, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.66
2019 Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Modelling structural constraints on protein evolution via side-chain conformational states. Molecular Biology and Evolution. PMID 31114882 DOI: 10.1093/Molbev/Msz122  0.307
2019 Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics (Oxford, England). 35: 462-469. PMID 30020414 DOI: 10.1093/bioinformatics/bty635  0.685
2018 Moal IH, Chaleil RAG, Bates PA. Flexible Protein-Protein Docking with SwarmDock. Methods in Molecular Biology (Clifton, N.J.). 1764: 413-428. PMID 29605931 DOI: 10.1007/978-1-4939-7759-8_27  0.469
2017 Barradas-Bautista D, Moal IH, Fernández-Recio J. A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining. Proteins. 85: 1287-1297. PMID 28342242 DOI: 10.1002/prot.25289  0.727
2017 Hayes TW, Moal IH. Modeling protein conformational transition pathways using collective motions and the LASSO method. Journal of Chemical Theory and Computation. PMID 28230364 DOI: 10.1021/acs.jctc.6b01110  0.387
2017 Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J. IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics (Oxford, England). PMID 28200016 DOI: 10.1093/Bioinformatics/Btx068  0.671
2016 Pallara C, Jiménez-García B, Romero M, Moal IH, Fernández-Recio J. pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions. Proteins. 85: 487-496. PMID 27701776 DOI: 10.1002/prot.25184  0.848
2016 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, ... ... Moal IH, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.841
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.736
2015 Moal IH, Dapkūnas J, Fernández-Recio J. Inferring the microscopic surface energy of protein-protein interfaces from mutation data. Proteins. 83: 640-50. PMID 25586563 DOI: 10.1002/prot.24761  0.627
2014 Moal IH, Fernández-Recio J. Comment on 'protein-protein binding affinity prediction from amino acid sequence'. Bioinformatics (Oxford, England). 31: 614-5. PMID 25381451 DOI: 10.1093/bioinformatics/btu682  0.697
2014 Moal IH, Jiménez-García B, Fernández-Recio J. CCharPPI web server: computational characterization of protein-protein interactions from structure. Bioinformatics (Oxford, England). 31: 123-5. PMID 25183488 DOI: 10.1093/bioinformatics/btu594  0.698
2014 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, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.764
2013 Moal IH, Fernandez-Recio J. Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation. Journal of Chemical Theory and Computation. 9: 3715-27. PMID 26584123 DOI: 10.1021/ct400295z  0.711
2013 Moal IH, Torchala M, Bates PA, Fernández-Recio J. The scoring of poses in protein-protein docking: current capabilities and future directions. Bmc Bioinformatics. 14: 286. PMID 24079540 DOI: 10.1186/1471-2105-14-286  0.733
2013 Agius R, Torchala M, Moal IH, Fernández-Recio J, Bates PA. Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. Plos Computational Biology. 9: e1003216. PMID 24039569 DOI: 10.1371/journal.pcbi.1003216  0.652
2013 Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins. 81: 2192-200. PMID 23934865 DOI: 10.1002/prot.24387  0.736
2013 Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Current Opinion in Structural Biology. 23: 862-7. PMID 23871100 DOI: 10.1016/J.Sbi.2013.06.017  0.731
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.781
2013 Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA. SwarmDock: a server for flexible protein-protein docking. Bioinformatics (Oxford, England). 29: 807-9. PMID 23343604 DOI: 10.1093/bioinformatics/btt038  0.707
2012 Moal IH, Fernández-Recio J. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. Bioinformatics (Oxford, England). 28: 2600-7. PMID 22859501 DOI: 10.1093/bioinformatics/bts489  0.743
2012 Moal IH, Bates PA. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. Plos Computational Biology. 8: e1002351. PMID 22253587 DOI: 10.1371/journal.pcbi.1002351  0.491
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.805
2011 Moal IH, Agius R, Bates PA. Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics (Oxford, England). 27: 3002-9. PMID 21903632 DOI: 10.1093/bioinformatics/btr513  0.466
2011 Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Science : a Publication of the Protein Society. 20: 482-91. PMID 21213247 DOI: 10.1002/Pro.580  0.423
2010 Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. International Journal of Molecular Sciences. 11: 3623-48. PMID 21152290 DOI: 10.3390/ijms11103623  0.399
2010 Li X, Moal IH, Bates PA. Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins. 78: 3189-96. PMID 20552581 DOI: 10.1002/prot.22770  0.429
2007 Melville JL, Moal IH, Baker-Glenn C, Shaw PE, Pattenden G, Hirst JD. The structural determinants of macrolide-actin binding: in silico insights. Biophysical Journal. 92: 3862-7. PMID 17351011 DOI: 10.1529/Biophysj.106.103580  0.301
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