ReviewBiophysical journal2019
Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins.
Review in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Boswellic Acid Derived Molecules as SARS-Cov-2 Spike Protein Inhibitors: A Comprehensive Virtual Screening, Triplicate Molecular Dynamic Simulation and Biochemical Validation.Current medicinal chemistry · 2026Article
- Discrete protein dynamics enable long-range communication.bioRxiv : the preprint server for biology · 2025Article
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- Identifying Rare Germline Variants Associated with Metastatic Prostate Cancer Through an Extreme Phenotype Study.medRxiv : the preprint server for health sciences · 2025Article
- The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.Topics in current chemistry (Cham) · 2024Review
- Identification of small molecular inhibitors of SIRT3 by computational and biochemical approaches a potential target of breast cancer.Scientific reports · 2024Article
- Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques.Scientific reports · 2024Article
- Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs.Journal of chemical information and modeling · 2023Article
- Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis.Journal of molecular modeling · 2023Article
- Thin-Plate Superstructures of the Immunogenic 33-mer Gliadin Peptide.Chembiochem : a European journal of chemical biology · 2022Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Methyl Viologens of Bis-(4'-Pyridylethynyl)Arenes - Structures, Photophysical and Electrochemical Studies, and their Potential Application in Biology.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Article
- Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction.International journal of molecular sciences · 2021Article
- A rotamer relay information system in the epidermal growth factor receptor-drug complexes reveals clues to new paradigm in protein conformational change.Computational and structural biotechnology journal · 2021Article
- Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability.PloS one · 2020Article
- Voltage vs. Ligand I: Structural basis of the intrinsic flexibility of S3 segment and its significance in ion channel activation.Channels (Austin, Tex.) · 2019Article
- The multifaceted helical net of amphipathic alpha-helices; the next dimension of the helical peptide wheel.Science progressArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.
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