ArticleJournal of chemical information and modeling2022
Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Inhibition of VEGFJournal of chemical information and modeling · 2026Article
- Divide and Cluster: The DIVINE Framework for Deterministic Top-Down Analysis of Molecular Dynamics Trajectories.Journal of chemical information and modeling · 2026Article
- Simulation-guided design of peptide-metal coordination interfaces for next-generation metallo-immunotherapy.Nano convergence · 2026Review
- Selector: A General Python Library for Diverse Subset Selection.Journal of chemical information and modeling · 2026Article
- Targeting epigenetic regulators: In-silico discovery of natural inhibitors against histone demethylase KDM4C.PloS one · 2026Article
- Structural Genomics Defines PBRM1 Bromodomain Variant Function in ccRCC.Human mutation · 2026Article
- Identification of Potential Nontoxic HumanACS omega · 2025Article
- Selector: A General Python Library for Diverse Subset Selection.bioRxiv : the preprint server for biology · 2025Article
- Multi-omics pan-cancer profiling of CDK2 andRSC advances · 2025Article
- Extended Quality (eQual): Radial Threshold Clustering Based onJournal of chemical information and modeling · 2025Article
- SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways.Journal of chemical information and modeling · 2025Article
- Molecular dynamics simulation in tissue engineering.BioImpacts : BI · 2025Review
- The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain.Protein science : a publication of the Protein Society · 2025Article
- Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Alternative weighting schemes for fine-tuned extended similarity indices.Journal of chemometrics · 2024Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) is a core methodology of molecular modeling and computational design for the study of the dynamics and temporal evolution of molecular systems. MD simulations have particularly benefited from the rapid increase of computational power that has characterized the past decades of computational chemical research, being the first method to be successfully migrated to the GPU infrastructure. While new-generation MD software is capable of delivering simulations on an ever-increasing scale, relatively less effort is invested in developing postprocessing methods that can keep up with the quickly expanding volumes of data that are being generated. Here, we introduce a new idea for sampling frames from large MD trajectories, based on the recently introduced framework of extended similarity indices. Our approach presents a new, linearly scaling alternative to the traditional approach of applying a clustering algorithm that usually scales as a quadratic function of the number of frames. When showcasing its usage on case studies with different system sizes and simulation lengths, we have registered speedups of up to 2 orders of magnitude, as compared to traditional clustering algorithms. The conformational diversity of the selected frames is also noticeably higher, which is a further advantage for certain applications, such as the selection of structural ensembles for ligand docking. The method is available open-source at https://github.com/ramirandaq/MultipleComparisons.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.