ArticleProceedings of the National Academy of Sciences of the United States of America2005
Molecular dynamics and protein function.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 411 papers.
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Who cites it
411 citing papers in PubMed, 1,140 citations in OpenAlex.
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- A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations.Scientific data · 2026Article
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- Integrated In Silico Prioritization of Antidiabetic Phytochemicals fromMolecules (Basel, Switzerland) · 2026Article
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- Making invisible excited-state structures of pro-interleukin-18 visible by combining NMR and machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Unveiling hidden intermediate states in protein folding with AI-based conditional transition clustering.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
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- Large Language Model Agent for Modular Task Execution in Drug Discovery.Journal of chemical information and modeling · 2026Article
- Article
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
351 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.
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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.