ArticleScientific reports2016
Quantifying side-chain conformational variations in protein structure.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Characterising Side Chain Conformations in Proteins UsingChemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Isoleucine Side Chains as Reporters of Conformational Freedom in Protein Folding Studied by DNP-Enhanced NMR.Journal of the American Chemical Society · 2025Article
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- Alternate conformations found in protein structures implies biological functions: A case study using cyclophilin A.Current research in structural biology · 2024Article
- Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels.Channels (Austin, Tex.) · 2023Article
- Improving Geometric Validation Metrics and Ensuring Consistency with Experimental Data through TrioSA: An NMR Refinement Protocol.International journal of molecular sciences · 2023Article
- Building protein structure-specific rotamer libraries.Bioinformatics (Oxford, England) · 2023Article
- GeoPacker: A novel deep learning framework for protein side-chain modeling.Protein science : a publication of the Protein Society · 2022Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Article
- CryoEM analysis of small plant biocatalysts at sub-2 Å resolution.Acta crystallographica. Section D, Structural biology · 2022Article
- Predicting TCR-Epitope Binding Specificity Using Deep Metric Learning and Multimodal Learning.Genes · 2021Article
- The genotype-phenotype landscape of an allosteric protein.Molecular systems biology · 2021Article
- 3D Interaction Homology: Computational Titration of Aspartic Acid, Glutamic Acid and Histidine Can Create pH-Tunable Hydropathic Environment Maps.Frontiers in molecular biosciences · 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
- FASPR: an open-source tool for fast and accurate protein side-chain packing.Bioinformatics (Oxford, England) · 2020Article
- PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1.Molecular informatics · 2020Article
- Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.Journal of chemical information and modeling · 2020Article
- SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models.PloS one · 2020Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.
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