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For: Borrelli KW, Cossins B, Guallar V. Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. J Comput Chem 2009;31:1224-35. [DOI: 10.1002/jcc.21409] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Nawa F, Sai M, Vietor J, Schwarzenbach R, Bitić A, Wolff S, Ildefeld N, Pabel J, Wein T, Marschner JA, Heering J, Merk D. Tuning RXR Modulators for PGC1α Recruitment. J Med Chem 2024;67:16338-16354. [PMID: 39258574 DOI: 10.1021/acs.jmedchem.4c01231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
2
Andrade C, Sousa BKDP, Sigurdardóttir S, Bourgard C, Borba J, Clementino L, Salazar-Alvarez LC, Groustra S, Zigweid R, Khim M, Staker B, Costa F, Eriksson L, Sunnerhagen P. Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase. RESEARCH SQUARE 2024:rs.3.rs-3963523. [PMID: 38463971 PMCID: PMC10925453 DOI: 10.21203/rs.3.rs-3963523/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
3
Acin‐Perez R, Benincá C, Fernandez del Rio L, Shu C, Baghdasarian S, Zanette V, Gerle C, Jiko C, Khairallah R, Khan S, Rincon Fernandez Pacheco D, Shabane B, Erion K, Masand R, Dugar S, Ghenoiu C, Schreiner G, Stiles L, Liesa M, Shirihai OS. Inhibition of ATP synthase reverse activity restores energy homeostasis in mitochondrial pathologies. EMBO J 2023;42:e111699. [PMID: 36912136 PMCID: PMC10183817 DOI: 10.15252/embj.2022111699] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 03/14/2023]  Open
4
Díaz-Rovira AM, Martín H, Beuming T, Díaz L, Guallar V, Ray SS. Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. J Chem Inf Model 2023;63:1668-1674. [PMID: 36892986 DOI: 10.1021/acs.jcim.2c01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
5
Beuming T, Martín H, Díaz-Rovira AM, Díaz L, Guallar V, Ray SS. Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. J Chem Inf Model 2022;62:4351-4360. [PMID: 36099477 DOI: 10.1021/acs.jcim.2c00796] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
6
Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
7
Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis. Nat Commun 2020;11:3216. [PMID: 32587248 PMCID: PMC7316778 DOI: 10.1038/s41467-020-17027-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/05/2020] [Indexed: 02/07/2023]  Open
8
Nešić D, Zhang Y, Spasic A, Li J, Provasi D, Filizola M, Walz T, Coller BS. Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex. Arterioscler Thromb Vasc Biol 2020;40:624-637. [PMID: 31969014 PMCID: PMC7047619 DOI: 10.1161/atvbaha.119.313671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/30/2019] [Indexed: 11/16/2022]
9
Cappel D, Jerome S, Hessler G, Matter H. Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. J Chem Inf Model 2020;60:1432-1444. [DOI: 10.1021/acs.jcim.9b01118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
10
Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths. Sci Rep 2019;9:17249. [PMID: 31754232 PMCID: PMC6872664 DOI: 10.1038/s41598-019-52319-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/11/2019] [Indexed: 12/18/2022]  Open
11
Matthews N, Kitao A, Laycock S, Hayward S. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. J Chem Inf Model 2019;59:2900-2912. [DOI: 10.1021/acs.jcim.9b00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
12
Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
13
Santiago G, Martínez-Martínez M, Alonso S, Bargiela R, Coscolín C, Golyshin PN, Guallar V, Ferrer M. Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry 2018;57:2245-2255. [DOI: 10.1021/acs.biochem.8b00274] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The INMARE Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol 2018;13:225-234. [PMID: 29182315 DOI: 10.1021/acschembio.7b00996] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Rogawski R, Sergeyev IV, Zhang Y, Tran TH, Li Y, Tong L, McDermott AE. NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples. J Phys Chem B 2017;121:10770-10781. [PMID: 29116793 PMCID: PMC5842680 DOI: 10.1021/acs.jpcb.7b08274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
16
Kotev M, Manuel-Manresa P, Hernando E, Soto-Cerrato V, Orozco M, Quesada R, Pérez-Tomás R, Guallar V. Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. J Chem Inf Model 2017;57:2089-2098. [PMID: 28763207 DOI: 10.1021/acs.jcim.7b00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
17
Adaptive simulations, towards interactive protein-ligand modeling. Sci Rep 2017;7:8466. [PMID: 28814780 PMCID: PMC5559483 DOI: 10.1038/s41598-017-08445-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022]  Open
18
Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Sci Rep 2017;7:8223. [PMID: 28811548 PMCID: PMC5557796 DOI: 10.1038/s41598-017-08344-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022]  Open
19
Sulimov AV, Zheltkov DA, Oferkin IV, Kutov DC, Katkova EV, Tyrtyshnikov EE, Sulimov VB. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. Comput Struct Biotechnol J 2017;15:275-285. [PMID: 28377797 PMCID: PMC5367798 DOI: 10.1016/j.csbj.2017.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/28/2017] [Indexed: 11/28/2022]  Open
20
Hayes TW, Moal IH. Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method. J Chem Theory Comput 2017;13:1401-1410. [DOI: 10.1021/acs.jctc.6b01110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
21
Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W. Relative Binding Free Energy Calculations Applied to Protein Homology Models. J Chem Inf Model 2016;56:2388-2400. [PMID: 28024402 PMCID: PMC5777225 DOI: 10.1021/acs.jcim.6b00362] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
22
The unravelling of the complex pattern of tyrosinase inhibition. Sci Rep 2016;6:34993. [PMID: 27725765 PMCID: PMC5057104 DOI: 10.1038/srep34993] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/22/2016] [Indexed: 12/28/2022]  Open
23
Massink A, Louvel J, Adlere I, van Veen C, Huisman BJH, Dijksteel GS, Guo D, Lenselink EB, Buckley BJ, Matthews H, Ranson M, Kelso M, IJzerman AP. 5′-Substituted Amiloride Derivatives as Allosteric Modulators Binding in the Sodium Ion Pocket of the Adenosine A2A Receptor. J Med Chem 2016;59:4769-77. [DOI: 10.1021/acs.jmedchem.6b00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
24
Hosseini A, Alibés A, Noguera-Julian M, Gil V, Paredes R, Soliva R, Orozco M, Guallar V. Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J Chem Inf Model 2016;56:915-23. [DOI: 10.1021/acs.jcim.5b00667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Grebner C, Iegre J, Ulander J, Edman K, Hogner A, Tyrchan C. Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design. J Chem Inf Model 2016;56:774-87. [DOI: 10.1021/acs.jcim.5b00744] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
26
Kotev M, Lecina D, Tarragó T, Giralt E, Guallar V. Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques. Biophys J 2015;108:116-25. [PMID: 25564858 DOI: 10.1016/j.bpj.2014.11.3453] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 01/03/2023]  Open
27
Madadkar-Sobhani A, Guallar V. PELE web server: atomistic study of biomolecular systems at your fingertips. Nucleic Acids Res 2013;41:W322-8. [PMID: 23729469 PMCID: PMC3692087 DOI: 10.1093/nar/gkt454] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
28
Hosseini A, Espona-Fiedler M, Soto-Cerrato V, Quesada R, Pérez-Tomás R, Guallar V. Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members. PLoS One 2013;8:e57562. [PMID: 23460874 PMCID: PMC3583838 DOI: 10.1371/journal.pone.0057562] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/26/2013] [Indexed: 12/03/2022]  Open
29
Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine. J Biol Chem 2011;286:41105-14. [PMID: 21940622 DOI: 10.1074/jbc.m111.282467] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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