ArticleJournal of computational chemistry2016
Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Structural insights into SOD1: from in silico and molecular dynamics to experimental analyses of ALS-associated E49K and R115G mutants.Frontiers in molecular biosciences · 2025Article
- In silico analysis of quorum sensing modulators: Insights into molecular docking and dynamics and potential therapeutic applications.PloS one · 2025Article
- k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations.bioRxiv : the preprint server for biology · 2024Article
- Structural Insights of PD-1/PD-L1 Axis: AnCurrent protein & peptide science · 2024Article
- Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking.Frontiers in molecular biosciences · 2023Article
- Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.Journal of molecular biology · 2022Article
- From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.Frontiers in pharmacology · 2022Review
- Article
- Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population.Scientific reports · 2021Article
- An atypical heterotrimeric Gα protein has substantially reduced nucleotide binding but retains nucleotide-independent interactions with its cognate RGS protein and Gβγ dimer.Journal of biomolecular structure & dynamics · 2020Article
- Flexibility of the petunia strigolactone receptor DAD2 promotes its interaction with signaling partners.The Journal of biological chemistry · 2020Article
- Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface.Biointerphases · 2017Article
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Authors and funding
5 authors.
Funding
Abstract
Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed-state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc.
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