ArticleProteins2014
Detecting local residue environment similarity for recognizing near-native structure models.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Using steered molecular dynamic tension for assessing quality of computational protein structure models.Journal of computational chemistry · 2022Article
- Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy.International journal of molecular sciences · 2021Article
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.The EMBO journal · 2020Article
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.Proteins · 2018Article
- Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.Proteins · 2017Article
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We developed a new representation of local amino acid environments in protein structures called the Side-chain Depth Environment (SDE). An SDE defines a local structural environment of a residue considering the coordinates and the depth of amino acids that locate in the vicinity of the side-chain centroid of the residue. SDEs are general enough that similar SDEs are found in protein structures with globally different folds. Using SDEs, we developed a procedure called PRESCO (Protein Residue Environment SCOre) for selecting native or near-native models from a pool of computational models. The procedure searches similar residue environments observed in a query model against a set of representative native protein structures to quantify how native-like SDEs in the model are. When benchmarked on commonly used computational model datasets, our PRESCO compared favorably with the other existing scoring functions in selecting native and near-native models.
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Registered trials
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