ArticleProteins2018
Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- GRAMM Web Server for Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.Chembiochem : a European journal of chemical biology · 2022Article
- GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.Journal of molecular biology · 2022Article
- Dockground scoring benchmarks for protein docking.Proteins · 2022Article
- AbAdapt: an adaptive approach to predicting antibody-antigen complex structures from sequence.Bioinformatics advances · 2022Article
- Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- ClusPro LigTBM: Automated Template-based Small Molecule Docking.Journal of molecular biology · 2020Article
- HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry.Journal of molecular biology · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.Bioinformatics (Oxford, England) · 2020Article
- Article
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Article
- Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.Biophysical journal · 2018Article
- Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.Journal of computer-aided molecular design · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
The paper presents analysis of our template-based and free docking predictions in the joint CASP12/CAPRI37 round. A new scoring function for template-based docking was developed, benchmarked on the Dockground resource, and applied to the targets. The results showed that the function successfully discriminates the incorrect docking predictions. In correctly predicted targets, the scoring function was complemented by other considerations, such as consistency of the oligomeric states among templates, similarity of the biological functions, biological interface relevance, etc. The scoring function still does not distinguish well biological from crystal packing interfaces, and needs further development for the docking of bundles of α-helices. In the case of the trimeric targets, sequence-based methods did not find common templates, despite similarity of the structures, suggesting complementary use of structure- and sequence-based alignments in comparative docking. The results showed that if a good docking template is found, an accurate model of the interface can be built even from largely inaccurate models of individual subunits. Free docking however is very sensitive to the quality of the individual models. However, our newly developed contact potential detected approximate locations of the binding sites.
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