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For: Ellis CR, Tsai CC, Hou X, Shen J. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 2016;7:944-9. [PMID: 26905811 PMCID: PMC5713896 DOI: 10.1021/acs.jpclett.6b00137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Number Cited by Other Article(s)
1
Wilson CJ, de Groot BL, Gapsys V. Resolving coupled pH titrations using alchemical free energy calculations. J Comput Chem 2024;45:1444-1455. [PMID: 38471815 DOI: 10.1002/jcc.27318] [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: 09/17/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 03/14/2024]
2
Schulke S, Nolten M, Schwaab G, Havenith M. Studying Local Electrostatics by Terahertz Spectroscopy Using Amines as a Probe. Chemphyschem 2024;25:e202300389. [PMID: 37897334 DOI: 10.1002/cphc.202300389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
3
Alcantara J, Chiu K, Bickel JD, Rizzo RC, Simmerling C. Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir. J Chem Theory Comput 2023;19:7934-7945. [PMID: 37831619 DOI: 10.1021/acs.jctc.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
4
Wang Y, Yang F, Yan D, Zeng Y, Wei B, Chen J, He W. Identification Mechanism of BACE1 on Inhibitors Probed by Using Multiple Separate Molecular Dynamics Simulations and Comparative Calculations of Binding Free Energies. Molecules 2023;28:4773. [PMID: 37375328 DOI: 10.3390/molecules28124773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]  Open
5
Onufriev AV. Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome. Front Mol Biosci 2023;10:1067787. [PMID: 37143824 PMCID: PMC10151541 DOI: 10.3389/fmolb.2023.1067787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/16/2023] [Indexed: 05/06/2023]  Open
6
Santos LH, Caffarena ER, Ferreira RS. pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations. J Biomol Struct Dyn 2022;40:10359-10372. [PMID: 34180376 DOI: 10.1080/07391102.2021.1943528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
7
Singh K, Muttathukattil AN, Singh PC, Reddy G. pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations. J Phys Chem B 2022;126:9759-9770. [PMID: 36383764 DOI: 10.1021/acs.jpcb.2c05117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
8
Henderson JA, Liu R, Harris JA, Huang Y, de Oliveira VM, Shen J. A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2022;4:1563. [PMID: 36776714 PMCID: PMC9910290 DOI: 10.33011/livecoms.4.1.1563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
9
Oliveira NF, Machuqueiro M. Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. J Chem Inf Model 2022;62:2550-2560. [PMID: 35442654 PMCID: PMC9775199 DOI: 10.1021/acs.jcim.2c00233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
10
do Bomfim MR, Barbosa DB, de Carvalho PB, da Silva AM, de Oliveira TA, Taranto AG, Leite FHA. Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2069155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
11
Hayes RL, Vilseck JZ, Brooks CL. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. J Chem Theory Comput 2022;18:2114-2123. [PMID: 35255214 PMCID: PMC9700482 DOI: 10.1021/acs.jctc.1c00948] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Henderson JA, Shen J. Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II. J Chem Inf Model 2021;62:150-158. [PMID: 34964641 DOI: 10.1021/acs.jcim.1c01180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Chen J, Zhang S, Wang W, Sun H, Zhang Q, Liu X. Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations. ACS Chem Neurosci 2021;12:2591-2607. [PMID: 34185514 DOI: 10.1021/acschemneuro.0c00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
14
Huang Y, Henderson JA, Shen J. Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins. Methods Mol Biol 2021;2302:275-287. [PMID: 33877633 PMCID: PMC8062021 DOI: 10.1007/978-1-0716-1394-8_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
15
Ugbaja SC, Sanusi ZK, Appiah-Kubi P, Lawal MM, Kumalo HM. Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment. Biophys Chem 2020;270:106536. [PMID: 33387910 DOI: 10.1016/j.bpc.2020.106536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/28/2022]
16
Henderson JA, Verma N, Harris RC, Liu R, Shen J. Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors. J Chem Phys 2020;153:115101. [PMID: 32962355 PMCID: PMC7499820 DOI: 10.1063/5.0020458] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
17
Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kalé LV, Schulten K, Chipot C, Tajkhorshid E. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys 2020;153:044130. [PMID: 32752662 PMCID: PMC7395834 DOI: 10.1063/5.0014475] [Citation(s) in RCA: 1242] [Impact Index Per Article: 310.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023]  Open
18
Henderson JA, Verma N, Shen J. Assessment of Proton-Coupled Conformational Dynamics of SARS and MERS Coronavirus Papain-like Proteases: Implication for Designing Broad-Spectrum Antiviral Inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.30.181305. [PMID: 32637952 PMCID: PMC7337382 DOI: 10.1101/2020.06.30.181305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
19
Chen J, Yin B, Wang W, Sun H. Effects of Disulfide Bonds on Binding of Inhibitors to β-Amyloid Cleaving Enzyme 1 Decoded by Multiple Replica Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2020;11:1811-1826. [PMID: 32459964 DOI: 10.1021/acschemneuro.0c00234] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
20
Sasmal S, El Khoury L, Mobley DL. D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. J Comput Aided Mol Des 2020;34:163-177. [PMID: 31781990 PMCID: PMC8208075 DOI: 10.1007/s10822-019-00249-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/06/2019] [Indexed: 01/05/2023]
21
Kawade R, Kuroda D, Tsumoto K. How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations. FEBS Lett 2019;594:903-912. [DOI: 10.1002/1873-3468.13674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/06/2019] [Indexed: 11/05/2022]
22
El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. J Comput Aided Mol Des 2019;33:1011-1020. [PMID: 31691919 PMCID: PMC7027993 DOI: 10.1007/s10822-019-00240-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022]
23
Harris RC, Shen J. GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations. J Chem Inf Model 2019;59:4821-4832. [PMID: 31661616 DOI: 10.1021/acs.jcim.9b00754] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
24
Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase. Protein Sci 2019;28:2080-2088. [PMID: 31610054 DOI: 10.1002/pro.3748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/25/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022]
25
Tsai CC, Yue Z, Shen J. How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase. J Am Chem Soc 2019;141:15092-15101. [PMID: 31476863 DOI: 10.1021/jacs.9b06064] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
26
Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019;141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
27
de Oliveira C, Yu HS, Chen W, Abel R, Wang L. Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States. J Chem Theory Comput 2018;15:424-435. [PMID: 30537823 DOI: 10.1021/acs.jctc.8b00826] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
28
Jagadeb M, Rath SN, Sonawane A. In silico discovery of potential drug molecules to improve the treatment of isoniazid-resistant Mycobacterium tuberculosis. J Biomol Struct Dyn 2018;37:3388-3398. [DOI: 10.1080/07391102.2018.1515116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
29
Bernetti M, Rosini E, Mollica L, Masetti M, Pollegioni L, Recanatini M, Cavalli A. Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. J Chem Inf Model 2018;58:2255-2265. [DOI: 10.1021/acs.jcim.8b00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
30
Henderson JA, Harris RC, Tsai CC, Shen J. How Ligand Protonation State Controls Water in Protein-Ligand Binding. J Phys Chem Lett 2018;9:5440-5444. [PMID: 30188715 PMCID: PMC6467052 DOI: 10.1021/acs.jpclett.8b02440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
31
Gueto-Tettay C, Martinez-Consuegra A, Pelaez-Bedoya L, Drosos-Ramirez JC. G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket. J Mol Graph Model 2018;85:1-12. [PMID: 30053756 DOI: 10.1016/j.jmgm.2018.07.008] [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: 05/17/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
32
Karch S, Broichhagen J, Schneider J, Böning D, Hartmann S, Schmid B, Tripal P, Palmisano R, Alzheimer C, Johnsson K, Huth T. A New Fluorogenic Small-Molecule Labeling Tool for Surface Diffusion Analysis and Advanced Fluorescence Imaging of β-Site Amyloid Precursor Protein-Cleaving Enzyme 1 Based on Silicone Rhodamine: SiR-BACE1. J Med Chem 2018;61:6121-6139. [PMID: 29939737 DOI: 10.1021/acs.jmedchem.8b00387] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
33
Atlam F, Awad M, Salama R. Factors Influencing the Potency of Alzheimer Inhibitors: Computational and Docking Studies. Am J Alzheimers Dis Other Demen 2018;33:166-175. [PMID: 29301410 PMCID: PMC10852456 DOI: 10.1177/1533317517749207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
34
Huang Y, Yue Z, Tsai CC, Henderson JA, Shen J. Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships. J Phys Chem Lett 2018;9:1179-1184. [PMID: 29461836 PMCID: PMC6555141 DOI: 10.1021/acs.jpclett.8b00238] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
35
Kilburg D, Gallicchio E. Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes. Front Mol Biosci 2018;5:22. [PMID: 29568737 PMCID: PMC5852065 DOI: 10.3389/fmolb.2018.00022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/21/2018] [Indexed: 01/24/2023]  Open
36
Harris RC, Tsai CC, Ellis CR, Shen J. Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase. J Phys Chem Lett 2017;8:4832-4837. [PMID: 28927275 PMCID: PMC5713904 DOI: 10.1021/acs.jpclett.7b02309] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
37
Huang J, Sun B, Yao Y, Liu J. Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad. J Chem Inf Model 2017;57:2273-2280. [DOI: 10.1021/acs.jcim.7b00207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
38
Prati F, Bottegoni G, Bolognesi ML, Cavalli A. BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease. J Med Chem 2017;61:619-637. [DOI: 10.1021/acs.jmedchem.7b00393] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
39
Ellis CR, Tsai CC, Lin FY, Shen J. Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. J Comput Chem 2017;38:1260-1269. [PMID: 28370344 PMCID: PMC5403572 DOI: 10.1002/jcc.24719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/21/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023]
40
Low JD, Bartberger MD, Chen K, Cheng Y, Fielden MR, Gore V, Hickman D, Liu Q, Allen Sickmier E, Vargas HM, Werner J, White RD, Whittington DA, Wood S, Minatti AE. Development of 2-aminooxazoline 3-azaxanthene β-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D. MEDCHEMCOMM 2017;8:1196-1206. [PMID: 30108829 PMCID: PMC6072065 DOI: 10.1039/c7md00106a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 12/20/2022]
41
Peng Y, Alexov E. Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes. Proteins 2017;85:282-295. [PMID: 27936518 PMCID: PMC9843452 DOI: 10.1002/prot.25221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/24/2016] [Accepted: 11/28/2016] [Indexed: 01/19/2023]
42
Kocak A, Erol I, Yildiz M, Can H. Computational insights into the protonation states of catalytic dyad in BACE1–acyl guanidine based inhibitor complex. J Mol Graph Model 2016;70:226-235. [DOI: 10.1016/j.jmgm.2016.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]
43
Sabbah DA, Zhong HA. Modeling the protonation states of β-secretase binding pocket by molecular dynamics simulations and docking studies. J Mol Graph Model 2016;68:206-215. [DOI: 10.1016/j.jmgm.2016.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/06/2016] [Accepted: 07/17/2016] [Indexed: 01/12/2023]
44
Perilla JR, Hadden JA, Goh BC, Mayne CG, Schulten K. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. J Phys Chem Lett 2016;7:1836-44. [PMID: 27128262 PMCID: PMC4876486 DOI: 10.1021/acs.jpclett.6b00517] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
45
Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Phys Chem Chem Phys 2016;18:24790-24801. [DOI: 10.1039/c6cp02097f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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