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For: Coleman RG, Sterling T, Weiss DR. SAMPL4 & DOCK3.7: lessons for automated docking procedures. J Comput Aided Mol Des 2014;28:201-9. [PMID: 24515818 DOI: 10.1007/s10822-014-9722-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/28/2014] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Cavasotto CN, Di Filippo JI. The Impact of Supervised Learning Methods in Ultralarge High-Throughput Docking. J Chem Inf Model 2023;63:2267-2280. [PMID: 37036491 DOI: 10.1021/acs.jcim.2c01471] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
2
Casbarra L, Procacci P. Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges. J Comput Aided Mol Des 2021;35:721-729. [PMID: 34027592 PMCID: PMC8141411 DOI: 10.1007/s10822-021-00388-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/03/2022]
3
Xu P, Sattasathuchana T, Guidez E, Webb SP, Montgomery K, Yasini H, Pedreira IFM, Gordon MS. Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm. J Chem Phys 2021;154:104122. [PMID: 33722015 PMCID: PMC7955858 DOI: 10.1063/5.0040759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/11/2021] [Indexed: 11/14/2022]  Open
4
Artificial intelligence in the early stages of drug discovery. Arch Biochem Biophys 2020;698:108730. [PMID: 33347838 DOI: 10.1016/j.abb.2020.108730] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
5
Jiang S, Feher M, Williams C, Cole B, Shaw DE. AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. J Chem Inf Model 2020;60:4326-4338. [PMID: 32639159 DOI: 10.1021/acs.jcim.0c00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
6
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des 2020;34:601-633. [PMID: 31984465 DOI: 10.1007/s10822-020-00290-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022]
7
Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nat Chem Biol 2017;14:126-134. [PMID: 29227473 PMCID: PMC5771956 DOI: 10.1038/nchembio.2527] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
8
Lapelosa M. Free Energy of Binding and Mechanism of Interaction for the MEEVD-TPR2A Peptide-Protein Complex. J Chem Theory Comput 2017;13:4514-4523. [PMID: 28723223 DOI: 10.1021/acs.jctc.7b00105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
9
Muniz HS, Nascimento AS. Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking. PLoS One 2017;12:e0174336. [PMID: 28323889 PMCID: PMC5360343 DOI: 10.1371/journal.pone.0174336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022]  Open
10
Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA. Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies. J Phys Chem B 2017;121:3458-3472. [PMID: 27966363 DOI: 10.1021/acs.jpcb.6b09198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations. J Comput Aided Mol Des 2016;30:707-730. [PMID: 27565797 PMCID: PMC5078160 DOI: 10.1007/s10822-016-9942-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/17/2016] [Indexed: 11/25/2022]
12
Lin JH. Review structure- and dynamics-based computational design of anticancer drugs. Biopolymers 2015;105:2-9. [DOI: 10.1002/bip.22744] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 01/13/2023]
13
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J Comput Aided Mol Des 2015;29:315-25. [PMID: 25726024 DOI: 10.1007/s10822-014-9795-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022]
14
The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des 2014;28:305-17. [PMID: 24599514 DOI: 10.1007/s10822-014-9735-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 01/21/2023]
15
Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. Blind prediction of HIV integrase binding from the SAMPL4 challenge. J Comput Aided Mol Des 2014;28:327-45. [PMID: 24595873 DOI: 10.1007/s10822-014-9723-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/11/2022]
16
Voet ARD, Kumar A, Berenger F, Zhang KYJ. Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. J Comput Aided Mol Des 2014;28:363-73. [PMID: 24446075 DOI: 10.1007/s10822-013-9702-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 12/17/2013] [Indexed: 12/14/2022]
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