ArticleJournal of molecular biology2008
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed, 179 citations in OpenAlex.
- OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information.Molecules (Basel, Switzerland) · 2025Article
- The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins.International journal of molecular sciences · 2023Article
- GeoPacker: A novel deep learning framework for protein side-chain modeling.Protein science : a publication of the Protein Society · 2022Article
- Structure Prediction, Evaluation, and Validation of GPR18 Lipid Receptor Using Free Programs.International journal of molecular sciences · 2022Article
- Multi-task learning to leverage partially annotated data for PPI interface prediction.Scientific reports · 2022Article
- OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors.Briefings in bioinformatics · 2022Article
- Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14.Proteins · 2022Article
- DeepRefiner: high-accuracy protein structure refinement by deep network calibration.Nucleic acids research · 2021Article
- Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14.Scientific reports · 2021Article
- InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network.Frontiers in bioinformatics · 2021Review
- Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off.Computational and structural biotechnology journal · 2021Article
- Using physical features of protein core packing to distinguish real proteins from decoys.Protein science : a publication of the Protein Society · 2020Article
- Article
- Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria.Microbial biotechnology · 2020Article
- An information gain-based approach for evaluating protein structure models.Computational and structural biotechnology journal · 2020Article
- Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13.Proteins · 2019Article
- Estimation of model accuracy in CASP13.Proteins · 2019Article
- Identification of native protein structures captured by principal interactions.BMC bioinformatics · 2019Article
- ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment.BMC bioinformatics · 2019Article
- OPUS-SSF: A side-chain-inclusive scoring function for ranking protein structural models.Protein science : a publication of the Protein Society · 2019Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement.
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Registered trials
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.