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For: 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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Number Cited by Other Article(s)
1
Chen L, Smith M, Roe DR, Miranda-Quintana RA. Extended Quality (eQual): Radial Threshold Clustering Based on n-ary Similarity. J Chem Inf Model 2025;65:5062-5070. [PMID: 40309753 DOI: 10.1021/acs.jcim.4c02341] [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: 05/02/2025]
2
Chen L, Leung JMG, Zsigmond K, Chong LT, Miranda-Quintana RA. SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways. J Chem Inf Model 2025;65:4775-4782. [PMID: 40326720 PMCID: PMC12107702 DOI: 10.1021/acs.jcim.5c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2025]
3
Kakoulidis P, Theotoki EI, Pantazopoulou VI, Vlachos IS, Emiris IZ, Stravopodis DJ, Anastasiadou E. Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins. Sci Rep 2025;15:9432. [PMID: 40108192 PMCID: PMC11923369 DOI: 10.1038/s41598-025-91849-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 02/24/2025] [Indexed: 03/22/2025]  Open
4
Pinheiro M, de Oliveira Bispo M, Mattos RS, Telles do Casal M, Chandra Garain B, Toldo JM, Mukherjee S, Barbatti M. ULaMDyn: enhancing excited-state dynamics analysis through streamlined unsupervised learning. DIGITAL DISCOVERY 2025;4:666-682. [PMID: 39885946 PMCID: PMC11774233 DOI: 10.1039/d4dd00374h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 01/07/2025] [Indexed: 02/01/2025]
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
Chen L, Roe DR, Miranda-Quintana RA. CADENCE: Clustering Algorithm - Density-based Exploration and Novelty Clustering with Efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639863. [PMID: 40060588 PMCID: PMC11888282 DOI: 10.1101/2025.02.24.639863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
7
Li X, Xiao X, Liu T. Key points for analyzing longitudinal twin growth discordance patterns and adverse perinatal outcomes. Am J Obstet Gynecol 2025:S0002-9378(25)00115-2. [PMID: 40015586 DOI: 10.1016/j.ajog.2025.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 02/21/2025] [Indexed: 03/01/2025]
8
Mondal K, Klauda JB. Publisher's Note: "Physically interpretable performance metrics for clustering" [J. Chem. Phys. 161, 244106 (2024)]. J Chem Phys 2025;162:069902. [PMID: 39927549 DOI: 10.1063/5.0260506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Indexed: 02/11/2025]  Open
9
Chen L, Leung JMG, Zsigmond K, Chong LT, Miranda-Quintana RA. SHINE: Deterministic Many-to-Many clustering of Molecular Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636541. [PMID: 39975301 PMCID: PMC11839051 DOI: 10.1101/2025.02.07.636541] [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: 02/21/2025]
10
Chen L, Smith M, Roe DR, Miranda-Quintana RA. Extended Quality (eQual): Radial threshold clustering based on n-ary similarity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.05.627001. [PMID: 39677679 PMCID: PMC11643124 DOI: 10.1101/2024.12.05.627001] [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: 12/17/2024]
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