• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4631607)   Today's Articles (3027)   Subscriber (49888)
For: Mukherjee S, Pantelopulos GA, Voelz VA. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking. Sci Rep 2016;6:31631. [PMID: 27538695 PMCID: PMC4990920 DOI: 10.1038/srep31631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Watanabe K, Zhao Q, Iwatsuki R, Fukui R, Ren W, Sugita Y, Nishida N. Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. J Am Chem Soc 2024;146:9790-9800. [PMID: 38549219 DOI: 10.1021/jacs.3c14383] [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: 04/11/2024]
2
Raddi RM, Voelz VA. Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding. J Phys Chem B 2023;127:10682-10690. [PMID: 38078851 DOI: 10.1021/acs.jpcb.3c04775] [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: 12/22/2023]
3
Mishra RP, Gupta S, Rathore AS, Goel G. Multi-Level High-Throughput Screening for Discovery of Ligands That Inhibit Insulin Aggregation. Mol Pharm 2022;19:3770-3783. [PMID: 36173709 DOI: 10.1021/acs.molpharmaceut.2c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
4
Mendoza-Martinez C, Papadourakis M, Llabrés S, Gupta AA, Barlow PN, Michel J. Energetics of a protein disorder-order transition in small molecule recognition. Chem Sci 2022;13:5220-5229. [PMID: 35655546 PMCID: PMC9093188 DOI: 10.1039/d2sc00028h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022]  Open
5
Paratope states in solution improve structure prediction and docking. Structure 2021;30:430-440.e3. [PMID: 34838187 DOI: 10.1016/j.str.2021.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/10/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022]
6
Das P, Mattaparthi VSK. Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study. ACS OMEGA 2020;5:8449-8462. [PMID: 32337406 PMCID: PMC7178334 DOI: 10.1021/acsomega.9b03372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/26/2020] [Indexed: 05/04/2023]
7
Al-Madhagi WM, Hashim NM, Awadh Ali NA, Taha H, Alhadi AA, Abdullah AA, Sharhan O, Othman R. Bioassay-Guided Isolation and in Silico Study of Antibacterial Compounds From Petroleum Ether Extract of Peperomia blanda (Jacq.) Kunth. J Chem Inf Model 2019;59:1858-1872. [PMID: 31117526 DOI: 10.1021/acs.jcim.8b00969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
8
Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR. Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. J Chem Theory Comput 2018;14:5459-5475. [PMID: 30240203 PMCID: PMC6571142 DOI: 10.1021/acs.jctc.8b00500] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
9
Liang H, Zhou G, Ge Y, D'Ambrosio EA, Eidem TM, Blanchard C, Shehatou C, Chatare VK, Dunman PM, Valentine AM, Voelz VA, Grimes CL, Andrade RB. Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus. Bioorg Med Chem 2018;26:3453-3460. [PMID: 29805074 PMCID: PMC6008248 DOI: 10.1016/j.bmc.2018.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/02/2018] [Accepted: 05/12/2018] [Indexed: 02/01/2023]
10
Åberg E, Karlsson OA, Andersson E, Jemth P. Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2. J Phys Chem B 2018;122:6899-6905. [DOI: 10.1021/acs.jpcb.8b03876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
11
Mittal S, Shukla D. Recruiting machine learning methods for molecular simulations of proteins. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1448976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
12
Unarta IC, Zhu L, Tse CKM, Cheung PPH, Yu J, Huang X. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Curr Opin Struct Biol 2018;49:54-62. [PMID: 29414512 DOI: 10.1016/j.sbi.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
13
Gianti E, Carnevale V. Computational Approaches to Studying Voltage-Gated Ion Channel Modulation by General Anesthetics. Methods Enzymol 2018;602:25-59. [DOI: 10.1016/bs.mie.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
14
Yadahalli S, Li J, Lane DP, Gosavi S, Verma CS. Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations. Sci Rep 2017;7:15600. [PMID: 29142290 PMCID: PMC5688104 DOI: 10.1038/s41598-017-15930-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022]  Open
15
Mittal S, Shukla D. Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity. J Phys Chem B 2017;121:9761-9770. [DOI: 10.1021/acs.jpcb.7b04785] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
16
Ciemny MP, Debinski A, Paczkowska M, Kolinski A, Kurcinski M, Kmiecik S. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction. Sci Rep 2016;6:37532. [PMID: 27905468 PMCID: PMC5131342 DOI: 10.1038/srep37532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/27/2016] [Indexed: 12/27/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA