ArticleProtein science : a publication of the Protein Society2007
OPUS-Ca: a knowledge-based potential function requiring only Calpha positions.
Article in Protein science : a publication of the Protein Society, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- MUfoldQA_G: High-accuracy protein model QA via retraining and transformation.Computational and structural biotechnology journal · 2021Article
- Binding site matching in rational drug design: algorithms and applications.Briefings in bioinformatics · 2019Review
- PSICA: a fast and accurate web service for protein model quality analysis.Nucleic acids research · 2019Article
- OPUS-SSF: A side-chain-inclusive scoring function for ranking protein structural models.Protein science : a publication of the Protein Society · 2019Article
- OPUS-CSF: A C-atom-based scoring function for ranking protein structural models.Protein science : a publication of the Protein Society · 2018Article
- OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.Journal of molecular biology · 2017Article
- DeepQA: improving the estimation of single protein model quality with deep belief networks.BMC bioinformatics · 2016Article
- Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.Proteins · 2016Article
- Selective refinement and selection of near-native models in protein structure prediction.Proteins · 2015Article
- A New Hidden Markov Model for Protein Quality Assessment Using Compatibility Between Protein Sequence and Structure.Tsinghua science and technology · 2015Article
- ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.BMC bioinformatics · 2014Article
- Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement.Proceedings of the ... Congress on Evolutionary Computation. Congress on Evolutionary Computation · 2014Article
- DL-PRO: A Novel Deep Learning Method for Protein Model Quality Assessment.Proceedings of ... International Joint Conference on Neural Networks. International Joint Conference on Neural Networks · 2014Article
- Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations.Bulletin of mathematical biology · 2013Article
- Protein structural model selection by combining consensus and single scoring methods.PloS one · 2013Article
- A position-specific distance-dependent statistical potential for protein structure and functional study.Structure (London, England : 1993) · 2012Article
- An iterative self-refining and self-evaluating approach for protein model quality estimation.Protein science : a publication of the Protein Society · 2012Article
- Prediction of protein tertiary structures using MUFOLD.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.PLoS computational biology · 2012Article
- Specificity quantification of biomolecular recognition and its implication for drug discovery.Scientific reports · 2012Article
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Authors and funding
5 authors.
Funding
Abstract
In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Calpha positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Calpha trace for auxiliary purposes. The potential function is formed based on seven major representative molecular interactions in proteins: distance-dependent pairwise energy with orientational preference, hydrogen bonding energy, short-range energy, packing energy, tri-peptide packing energy, three-body energy, and solvation energy. From the testing of decoy recognition on a number of commonly used decoy sets, it is shown that the new potential function outperforms all known Calpha-based potentials and most other coarse-grained ones that require more information than Calpha positions. We hope that this potential function adds a new tool for protein structural modeling.
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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.