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For: Klem H, Hocky GM, McCullagh M. Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories. J Chem Theory Comput 2022;18:3218-3230. [PMID: 35483073 DOI: 10.1021/acs.jctc.1c01290] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Peña Ccoa WJ, Mukadum F, Ramon A, Stirnemann G, Hocky GM. A direct computational assessment of vinculin-actin unbinding kinetics reveals catch-bonding behavior. Proc Natl Acad Sci U S A 2025;122:e2425982122. [PMID: 40397673 DOI: 10.1073/pnas.2425982122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 04/16/2025] [Indexed: 05/23/2025]  Open
2
Yamamoto Y. Algorithm for Efficient Superposition and Clustering of Molecular Assemblies Using the Branch-and-Bound Method. J Chem Inf Model 2025;65:4512-4530. [PMID: 40276894 DOI: 10.1021/acs.jcim.4c02217] [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: 04/26/2025]
3
Zakir M, LeVatte MA, Wishart DS. RT-Pred: A web server for accurate, customized liquid chromatography retention time prediction of chemicals. J Chromatogr A 2025;1747:465816. [PMID: 40023050 DOI: 10.1016/j.chroma.2025.465816] [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: 12/16/2024] [Revised: 02/21/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
4
Sasmal S, McCullagh M, Hocky GM. Improved data-driven collective variables for biased sampling through iteration on biased data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.25.644418. [PMID: 40196594 PMCID: PMC11974779 DOI: 10.1101/2025.03.25.644418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
5
Chen L, Santos JBW, Gaza J, Perez A, Miranda-Quintana RA. Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.05.641742. [PMID: 40161705 PMCID: PMC11952300 DOI: 10.1101/2025.03.05.641742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
6
Liu B, Boysen JG, Unarta IC, Du X, Li Y, Huang X. Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space. Nat Commun 2025;16:349. [PMID: 39753544 PMCID: PMC11699157 DOI: 10.1038/s41467-024-55228-4] [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: 06/07/2024] [Accepted: 12/05/2024] [Indexed: 01/06/2025]  Open
7
Mondal K, Klauda JB. Physically interpretable performance metrics for clustering. J Chem Phys 2024;161:244106. [PMID: 39723706 DOI: 10.1063/5.0241122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Accepted: 11/21/2024] [Indexed: 12/28/2024]  Open
8
França VLB, Amaral JL, do Ó Pessoa C, Carvalho HF, Freire VN. Shedding light on cancer immunology at the molecular level: A quantum biochemistry study of representative PD-1/PD-L1 conformations. Biochem Biophys Res Commun 2024;735:150832. [PMID: 39423575 DOI: 10.1016/j.bbrc.2024.150832] [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: 06/25/2024] [Revised: 09/06/2024] [Accepted: 10/12/2024] [Indexed: 10/21/2024]
9
França VLB, Bezerra EM, da Costa RF, Carvalho HF, Freire VN, Matos G. Alzheimer's Disease Immunotherapy and Mimetic Peptide Design for Drug Development: Mutation Screening, Molecular Dynamics, and a Quantum Biochemistry Approach Focusing on Aducanumab::Aβ2-7 Binding Affinity. ACS Chem Neurosci 2024;15:3543-3562. [PMID: 39302203 PMCID: PMC11450751 DOI: 10.1021/acschemneuro.4c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]  Open
10
Akgüller Ö, Balcı MA, Cioca G. Clustering Molecules at a Large Scale: Integrating Spectral Geometry with Deep Learning. Molecules 2024;29:3902. [PMID: 39202980 PMCID: PMC11357287 DOI: 10.3390/molecules29163902] [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: 07/20/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024]  Open
11
Mukadum F, Ccoa WJP, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Cytoskeleton (Hoboken) 2024;81:318-327. [PMID: 38334204 PMCID: PMC11310368 DOI: 10.1002/cm.21837] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
12
Mazzaferro N, Sasmal S, Cossio P, Hocky GM. Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach. J Chem Theory Comput 2024;20:5901-5912. [PMID: 38954555 PMCID: PMC11270837 DOI: 10.1021/acs.jctc.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
13
Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase. Nucleic Acids Res 2024;52:7447-7464. [PMID: 38884215 PMCID: PMC11260461 DOI: 10.1093/nar/gkae500] [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] [Received: 12/01/2023] [Revised: 05/11/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]  Open
14
Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations. J Chem Theory Comput 2024;20:5583-5597. [PMID: 38905589 PMCID: PMC11541788 DOI: 10.1021/acs.jctc.4c00308] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
15
Sasmal S, Pal T, Hocky GM, McCullagh M. Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM. J Chem Theory Comput 2024;20:3492-3502. [PMID: 38662196 PMCID: PMC11104435 DOI: 10.1021/acs.jctc.4c00223] [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] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
16
Gallegos M, Isamura BK, Popelier PLA, Martín Pendás Á. An Unsupervised Machine Learning Approach for the Automatic Construction of Local Chemical Descriptors. J Chem Inf Model 2024;64:3059-3079. [PMID: 38498942 PMCID: PMC11040729 DOI: 10.1021/acs.jcim.3c01906] [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] [Received: 11/27/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
17
Wu Y, Cao S, Qiu Y, Huang X. Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes. J Chem Phys 2024;160:121501. [PMID: 38516972 PMCID: PMC10964226 DOI: 10.1063/5.0189429] [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] [Received: 11/28/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024]  Open
18
Daniel DT, Mitra S, Eichel RA, Diddens D, Granwehr J. Machine Learning Isotropic g Values of Radical Polymers. J Chem Theory Comput 2024;20:2592-2604. [PMID: 38456629 DOI: 10.1021/acs.jctc.3c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
19
Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583975. [PMID: 38496504 PMCID: PMC10942464 DOI: 10.1101/2024.03.07.583975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
20
Lawal MM, Roy P, McCullagh M. Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. J Phys Chem B 2024;128:492-503. [PMID: 38175211 PMCID: PMC11256563 DOI: 10.1021/acs.jpcb.3c06714] [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: 01/05/2024]
21
Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569434. [PMID: 38077049 PMCID: PMC10705498 DOI: 10.1101/2023.11.30.569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
22
Lawal MM, Roy P, McCullagh M. The Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560057. [PMID: 37808802 PMCID: PMC10557736 DOI: 10.1101/2023.09.28.560057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
23
Wellawatte GP, Hocky GM, White AD. Neural potentials of proteins extrapolate beyond training data. J Chem Phys 2023;159:085103. [PMID: 37642255 PMCID: PMC10474891 DOI: 10.1063/5.0147240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]  Open
24
Appadurai R, Koneru JK, Bonomi M, Robustelli P, Srivastava A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding. J Chem Theory Comput 2023;19:4711-4727. [PMID: 37338049 PMCID: PMC11108026 DOI: 10.1021/acs.jctc.3c00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
25
Sasmal S, McCullagh M, Hocky GM. Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions. J Chem Theory Comput 2023;19:4427-4435. [PMID: 37130367 PMCID: PMC10373481 DOI: 10.1021/acs.jctc.3c00051] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/04/2023]
26
Nagel D, Sartore S, Stock G. Selecting Features for Markov Modeling: A Case Study on HP35. J Chem Theory Comput 2023. [PMID: 37167425 DOI: 10.1021/acs.jctc.3c00240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
27
Dominic AJ, Cao S, Montoya-Castillo A, Huang X. Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently. J Am Chem Soc 2023;145:9916-9927. [PMID: 37104720 DOI: 10.1021/jacs.3c01095] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
28
Dominic AJ, Sayer T, Cao S, Markland TE, Huang X, Montoya-Castillo A. Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proc Natl Acad Sci U S A 2023;120:e2221048120. [PMID: 36920924 PMCID: PMC10041170 DOI: 10.1073/pnas.2221048120] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023]  Open
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