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Items: 33

1.

Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.

Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH.

Mol Biol Evol. 2019 Sep 1;36(9):2086-2103. doi: 10.1093/molbev/msz122.

2.

SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.

Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH.

Bioinformatics. 2019 Feb 1;35(3):462-469. doi: 10.1093/bioinformatics/bty635.

3.

Flexible Protein-Protein Docking with SwarmDock.

Moal IH, Chaleil RAG, Bates PA.

Methods Mol Biol. 2018;1764:413-428. doi: 10.1007/978-1-4939-7759-8_27.

PMID:
29605931
4.

A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.

Barradas-Bautista D, Moal IH, Fernández-Recio J.

Proteins. 2017 Jul;85(7):1287-1297. doi: 10.1002/prot.25289. Epub 2017 Apr 12.

PMID:
28342242
5.

Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.

Hayes TW, Moal IH.

J Chem Theory Comput. 2017 Mar 14;13(3):1401-1410. doi: 10.1021/acs.jctc.6b01110. Epub 2017 Mar 3.

PMID:
28230364
6.

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J.

Bioinformatics. 2017 Jun 15;33(12):1806-1813. doi: 10.1093/bioinformatics/btx068.

7.

A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.

Pfeiffenberger E, Chaleil RA, Moal IH, Bates PA.

Proteins. 2017 Mar;85(3):528-543. doi: 10.1002/prot.25218. Epub 2017 Jan 20.

8.

pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions.

Pallara C, Jiménez-García B, Romero M, Moal IH, Fernández-Recio J.

Proteins. 2017 Mar;85(3):487-496. doi: 10.1002/prot.25184. Epub 2016 Oct 25.

PMID:
27701776
9.

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, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

10.

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

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.

J Mol Biol. 2015 Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. Epub 2015 Jul 29.

11.

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

Moal IH, Dapkūnas J, Fernández-Recio J.

Proteins. 2015 Apr;83(4):640-50. doi: 10.1002/prot.24761. Epub 2015 Feb 5.

PMID:
25586563
12.

Comment on 'protein-protein binding affinity prediction from amino acid sequence'.

Moal IH, Fernández-Recio J.

Bioinformatics. 2015 Feb 15;31(4):614-5. doi: 10.1093/bioinformatics/btu682. Epub 2014 Oct 17. No abstract available.

PMID:
25381451
13.

The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.

Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X.

Mol Microbiol. 2015 Jan;95(1):17-30. doi: 10.1111/mmi.12844. Epub 2014 Nov 24.

14.

CCharPPI web server: computational characterization of protein-protein interactions from structure.

Moal IH, Jiménez-García B, Fernández-Recio J.

Bioinformatics. 2015 Jan 1;31(1):123-5. doi: 10.1093/bioinformatics/btu594. Epub 2014 Sep 2.

PMID:
25183488
15.

Prediction of Kunitz ion channel effectors and protease inhibitors from the Ixodes ricinus sialome.

Valdés JJ, Moal IH.

Ticks Tick Borne Dis. 2014 Oct;5(6):947-50. doi: 10.1016/j.ttbdis.2014.07.016. Epub 2014 Jul 29.

PMID:
25108785
16.

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, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

17.

The scoring of poses in protein-protein docking: current capabilities and future directions.

Moal IH, Torchala M, Bates PA, Fernández-Recio J.

BMC Bioinformatics. 2013 Oct 1;14:286. doi: 10.1186/1471-2105-14-286.

18.

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.

Agius R, Torchala M, Moal IH, Fernández-Recio J, Bates PA.

PLoS Comput Biol. 2013;9(9):e1003216. doi: 10.1371/journal.pcbi.1003216. Epub 2013 Sep 5.

19.

Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges.

Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J.

Proteins. 2013 Dec;81(12):2192-200. doi: 10.1002/prot.24387. Epub 2013 Oct 17.

PMID:
23934865
20.

Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation.

Moal IH, Fernandez-Recio J.

J Chem Theory Comput. 2013 Aug 13;9(8):3715-27. doi: 10.1021/ct400295z. Epub 2013 Jul 3.

PMID:
26584123
21.

A Markov-chain model description of binding funnels to enhance the ranking of docked solutions.

Torchala M, Moal IH, Chaleil RA, Agius R, Bates PA.

Proteins. 2013 Dec;81(12):2143-9. doi: 10.1002/prot.24369. Epub 2013 Sep 10.

PMID:
23900714
22.

Scoring functions for protein-protein interactions.

Moal IH, Moretti R, Baker D, Fernández-Recio J.

Curr Opin Struct Biol. 2013 Dec;23(6):862-7. doi: 10.1016/j.sbi.2013.06.017. Epub 2013 Jul 18. Review.

PMID:
23871100
23.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

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, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

24.

SwarmDock: a server for flexible protein-protein docking.

Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA.

Bioinformatics. 2013 Mar 15;29(6):807-9. doi: 10.1093/bioinformatics/btt038. Epub 2013 Jan 23.

PMID:
23343604
25.

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.

Moal IH, Fernández-Recio J.

Bioinformatics. 2012 Oct 15;28(20):2600-7. doi: 10.1093/bioinformatics/bts489. Epub 2012 Aug 1.

PMID:
22859501
26.

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

Moal IH, Bates PA.

PLoS Comput Biol. 2012 Jan;8(1):e1002351. doi: 10.1371/journal.pcbi.1002351. Epub 2012 Jan 12.

27.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

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, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.

J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29.

28.

Protein-protein binding affinity prediction on a diverse set of structures.

Moal IH, Agius R, Bates PA.

Bioinformatics. 2011 Nov 1;27(21):3002-9. doi: 10.1093/bioinformatics/btr513. Epub 2011 Sep 7.

PMID:
21903632
29.

A structure-based benchmark for protein-protein binding affinity.

Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J.

Protein Sci. 2011 Mar;20(3):482-91. doi: 10.1002/pro.580. Epub 2011 Feb 16.

30.

SwarmDock and the use of normal modes in protein-protein docking.

Moal IH, Bates PA.

Int J Mol Sci. 2010 Sep 28;11(10):3623-48. doi: 10.3390/ijms11103623.

31.

Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding.

Li X, Moal IH, Bates PA.

Proteins. 2010 Nov 15;78(15):3189-96. doi: 10.1002/prot.22770.

PMID:
20552581
32.

The structural determinants of macrolide-actin binding: in silico insights.

Melville JL, Moal IH, Baker-Glenn C, Shaw PE, Pattenden G, Hirst JD.

Biophys J. 2007 Jun 1;92(11):3862-7. Epub 2007 Mar 9.

33.

Effects of ulapualide A and synthetic macrolide analogues on actin dynamics and gene regulation.

Vincent E, Saxton J, Baker-Glenn C, Moal I, Hirst JD, Pattenden G, Shaw PE.

Cell Mol Life Sci. 2007 Feb;64(4):487-97.

PMID:
17279315

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