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For: Kongsted J, Söderhjelm P, Ryde U. How accurate are continuum solvation models for drug-like molecules? J Comput Aided Mol Des 2009;23:395-409. [DOI: 10.1007/s10822-009-9271-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 04/15/2009] [Indexed: 12/01/2022]
Number Cited by Other Article(s)
1
Adokoh CK, Boadu A, Asiamah I, Agoni C. Synthesis and characterization of gold(I) thiolate derivatives and bimetallic complexes for HIV inhibition. Front Chem 2024;12:1424019. [PMID: 39119520 PMCID: PMC11306053 DOI: 10.3389/fchem.2024.1424019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/01/2024] [Indexed: 08/10/2024]  Open
2
Bowleg JL, Mikek CG, Gwaltney SR. Computed interactions of berenil with restricted foldamers of c-MYC DNA G-quadruplexes. J Biomol Struct Dyn 2024;42:2162-2169. [PMID: 37286380 DOI: 10.1080/07391102.2023.2217913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/16/2023] [Indexed: 06/09/2023]
3
Dean E, Dominique A, Palillero A, Tran A, Paradis N, Wu C. Probing the Activation Mechanisms of Agonist DPI-287 to Delta-Opioid Receptor and Novel Agonists Using Ensemble-Based Virtual Screening with Molecular Dynamics Simulations. ACS OMEGA 2023;8:32404-32423. [PMID: 37720760 PMCID: PMC10500586 DOI: 10.1021/acsomega.3c01918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
4
Uba AI, Bui-Linh C, Thornton JM, Olivieri M, Wu C. Computational analysis of drug resistance of taxanes bound to human β-tubulin mutant (D26E). J Mol Graph Model 2023;123:108503. [PMID: 37209440 DOI: 10.1016/j.jmgm.2023.108503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/22/2023]
5
Yan F, Fu Z, Li G, Wang Z. In Silico Investigation of the Molecular Mechanism of PARP1 Inhibition for the Treatment of BRCA-Deficient Cancers. Molecules 2023;28:1829. [PMID: 36838818 PMCID: PMC9961911 DOI: 10.3390/molecules28041829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]  Open
6
Wang Y, Li G, Meng T, Qi L, Yan H, Wang Z. Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex. J Mol Graph Model 2021;110:108058. [PMID: 34736054 DOI: 10.1016/j.jmgm.2021.108058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022]
7
Leung L, Liao S, Wu C. To Probe the Binding Interactions between Two FDA Approved Migraine Drugs (Ubrogepant and Rimegepant) and Calcitonin-Gene Related Peptide Receptor (CGRPR) Using Molecular Dynamics Simulations. ACS Chem Neurosci 2021;12:2629-2642. [PMID: 34184869 DOI: 10.1021/acschemneuro.1c00135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
8
Fortuna A, Costa PJ. Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges. J Chem Inf Model 2021;61:3361-3375. [PMID: 34185532 DOI: 10.1021/acs.jcim.1c00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
9
Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach. J Mol Model 2021;27:160. [PMID: 33963942 PMCID: PMC8105700 DOI: 10.1007/s00894-021-04750-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/15/2021] [Indexed: 12/26/2022]
10
Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021;23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
11
Abdjan MI, Aminah NS, Siswanto I, Thant TM, Kristanti AN, Takaya Y. In silico approach: biological prediction of nordentatin derivatives as anticancer agent inhibitors in the cAMP pathway. RSC Adv 2020;10:42733-42743. [PMID: 35514899 PMCID: PMC9058016 DOI: 10.1039/d0ra07838g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/06/2020] [Indexed: 11/23/2022]  Open
12
Wang Z, Li G, Tian Z, Lou X, Huang Y, Wang L, Li J, Hou T, Liu JP. Insight Derived from Molecular Dynamics Simulation into the Selectivity Mechanism Targeting c-MYC G-Quadruplex. J Phys Chem B 2020;124:9773-9784. [DOI: 10.1021/acs.jpcb.0c05029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
13
Uba AI, Radicella C, Readmond C, Scorese N, Liao S, Liu H, Wu C. Binding of agonist WAY-267,464 and antagonist WAY-methylated to oxytocin receptor probed by all-atom molecular dynamics simulations. Life Sci 2020;252:117643. [DOI: 10.1016/j.lfs.2020.117643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 01/07/2023]
14
Chen B, Fountain G, Sullivan HJ, Paradis N, Wu C. To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis. Phys Chem Chem Phys 2020;22:22567-22583. [DOI: 10.1039/d0cp03863f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
15
Xu L, Coote ML. Improving the Accuracy of PCM-UAHF and PCM-UAKS Calculations Using Optimized Electrostatic Scaling Factors. J Chem Theory Comput 2019;15:6958-6967. [DOI: 10.1021/acs.jctc.9b00888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
16
Wang E, Weng G, Sun H, Du H, Zhu F, Chen F, Wang Z, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions. Phys Chem Chem Phys 2019;21:18958-18969. [PMID: 31453590 DOI: 10.1039/c9cp04096j] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
17
Nunes R, Vila-Viçosa D, Costa PJ. Tackling Halogenated Species with PBSA: Effect of Emulating the σ-Hole. J Chem Theory Comput 2019;15:4241-4251. [PMID: 31142112 DOI: 10.1021/acs.jctc.9b00106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
18
Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. Molecules 2019;24:molecules24061010. [PMID: 30871220 PMCID: PMC6471034 DOI: 10.3390/molecules24061010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/01/2019] [Accepted: 03/09/2019] [Indexed: 11/30/2022]  Open
19
Sullivan HJ, Readmond C, Radicella C, Persad V, Fasano TJ, Wu C. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS OMEGA 2018;3:14788-14806. [PMID: 30555989 PMCID: PMC6289566 DOI: 10.1021/acsomega.8b01574] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
20
Orr AA, Shaykhalishahi H, Mirecka EA, Jonnalagadda SVR, Hoyer W, Tamamis P. Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins. Comput Chem Eng 2018;116:322-332. [PMID: 30405276 PMCID: PMC6217933 DOI: 10.1016/j.compchemeng.2018.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
21
Gohda K. An attempt to incorporate effect of direct interaction between a ligand and explicit water molecules into MM/3D-RISM. Chem Biol Drug Des 2018;92:1788-1800. [PMID: 29962020 DOI: 10.1111/cbdd.13347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/12/2018] [Accepted: 05/28/2018] [Indexed: 11/28/2022]
22
Sader S, Anant K, Wu C. To probe interaction of morphine and IBNtxA with 7TM and 6TM variants of the human μ-opioid receptor using all-atom molecular dynamics simulations with an explicit membrane. Phys Chem Chem Phys 2018;20:1724-1741. [PMID: 29265141 DOI: 10.1039/c7cp06745c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
23
Mulholland K, Siddiquei F, Wu C. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent. Phys Chem Chem Phys 2018;19:18685-18694. [PMID: 28696445 DOI: 10.1039/c7cp03313c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
24
Readmond C, Wu C. Investigating detailed interactions between novel PAR1 antagonist F16357 and the receptor using docking and molecular dynamic simulations. J Mol Graph Model 2017;77:205-217. [DOI: 10.1016/j.jmgm.2017.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 01/08/2023]
25
Sader S, Wu C. Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent. J Mol Graph Model 2017;72:209-219. [DOI: 10.1016/j.jmgm.2016.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/07/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
26
Stasyuk OA, Jakubec D, Vondrášek J, Hobza P. Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes. J Chem Theory Comput 2017;13:877-885. [PMID: 27992205 DOI: 10.1021/acs.jctc.6b00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
27
Capilato JN, Philippi SV, Reardon T, McConnell A, Oliver DC, Warren A, Adams JS, Wu C, Perez LJ. Development of a novel series of non-natural triaryl agonists and antagonists of the Pseudomonas aeruginosa LasR quorum sensing receptor. Bioorg Med Chem 2016;25:153-165. [PMID: 27825554 DOI: 10.1016/j.bmc.2016.10.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
28
Zhang H, Yin C, Yan H, van der Spoel D. Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host–Guest Complexes. J Chem Inf Model 2016;56:2080-2092. [DOI: 10.1021/acs.jcim.6b00418] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Mulholland K, Wu C. Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. J Chem Inf Model 2016;56:2093-2102. [DOI: 10.1021/acs.jcim.6b00473] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
30
Spiliotopoulos D, Kastritis PL, Melquiond ASJ, Bonvin AMJJ, Musco G, Rocchia W, Spitaleri A. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Front Mol Biosci 2016;3:46. [PMID: 27630991 PMCID: PMC5006095 DOI: 10.3389/fmolb.2016.00046] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/16/2016] [Indexed: 11/13/2022]  Open
31
Zheng X, Wu C, Liu D, Li H, Bitan G, Shea JE, Bowers MT. Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? J Phys Chem B 2015;120:1615-23. [PMID: 26439281 DOI: 10.1021/acs.jpcb.5b08177] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
32
Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 2015;10:449-61. [PMID: 25835573 PMCID: PMC4487606 DOI: 10.1517/17460441.2015.1032936] [Citation(s) in RCA: 2705] [Impact Index Per Article: 300.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
33
Van de Vijver R, Vandewiele NM, Bhoorasingh PL, Slakman BL, Seyedzadeh Khanshan F, Carstensen HH, Reyniers MF, Marin GB, West RH, Van Geem KM. Automatic Mechanism and Kinetic Model Generation for Gas- and Solution-Phase Processes: A Perspective on Best Practices, Recent Advances, and Future Challenges. INT J CHEM KINET 2015. [DOI: 10.1002/kin.20902] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
34
Kumari R, Kumar R, Lynn A. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 2014;54:1951-62. [PMID: 24850022 DOI: 10.1021/ci500020m] [Citation(s) in RCA: 3055] [Impact Index Per Article: 305.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
35
Botello-Smith WM, Cai Q, Luo R. Biological applications of classical electrostatics methods. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614400082] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
36
Mikulskis P, Genheden S, Ryde U. Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach. J Mol Model 2014;20:2273. [DOI: 10.1007/s00894-014-2273-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/24/2014] [Indexed: 12/24/2022]
37
Wen M, Jiang J, Wang ZX, Wu C. How accurate are the popular PCM/GB continuum solvation models for calculating the solvation energies of amino acid side-chain analogs? Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1471-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
38
Guardia CM, Caramelo JJ, Trujillo M, Méndez-Huergo SP, Radi R, Estrin DA, Rabinovich GA. Structural basis of redox-dependent modulation of galectin-1 dynamics and function. Glycobiology 2014;24:428-41. [PMID: 24451991 DOI: 10.1093/glycob/cwu008] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
39
Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? J Mol Graph Model 2013;46:41-51. [DOI: 10.1016/j.jmgm.2013.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 11/20/2022]
40
Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides. PLoS Comput Biol 2013;9:e1003211. [PMID: 24009497 PMCID: PMC3757079 DOI: 10.1371/journal.pcbi.1003211] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/20/2013] [Indexed: 12/22/2022]  Open
41
Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors. J Mol Graph Model 2013;44:44-53. [DOI: 10.1016/j.jmgm.2013.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/09/2013] [Accepted: 05/01/2013] [Indexed: 11/20/2022]
42
Kalyaanamoorthy S, Chen YPP. Modelling and enhanced molecular dynamics to steer structure-based drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013;114:123-36. [PMID: 23827463 DOI: 10.1016/j.pbiomolbio.2013.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/31/2013] [Accepted: 06/22/2013] [Indexed: 10/26/2022]
43
Kolář M, Fanfrlík J, Lepšík M, Forti F, Luque FJ, Hobza P. Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches. J Phys Chem B 2013;117:5950-62. [PMID: 23600402 DOI: 10.1021/jp402117c] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
44
Remko M, Bojarska J, Ježko P, Maniukiewicz W, Olczak A. Molecular structure of antihypertensive drug perindopril, its active metabolite perindoprilat and impurity F. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.11.070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
45
Remko M, Duijnen PTV, Broer R. Structure and stability of complexes of charged structural units of heparin with arginine and lysine. RSC Adv 2013. [DOI: 10.1039/c2ra22062h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
46
Genheden S, Kuhn O, Mikulskis P, Hoffmann D, Ryde U. The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J Chem Inf Model 2012;52:2079-88. [DOI: 10.1021/ci3001919] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
47
Lei H, Wang X, Wu C. Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Model 2012;38:279-89. [PMID: 23079648 DOI: 10.1016/j.jmgm.2012.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/06/2012] [Accepted: 05/15/2012] [Indexed: 11/19/2022]
48
Genheden S, Ryde U. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies. Proteins 2012;80:1326-42. [PMID: 22274991 DOI: 10.1002/prot.24029] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 11/10/2022]
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Homeyer N, Gohlke H. Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method. Mol Inform 2012;31:114-22. [DOI: 10.1002/minf.201100135] [Citation(s) in RCA: 603] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/26/2011] [Indexed: 11/06/2022]
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Poisson–Boltzmann Implicit Solvation Models. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-444-59440-2.00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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