ArticleProteins2020
Application of docking methodologies to modeled proteins.
Article in Proteins, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Integrating deep learning with physics based modeling enables high precision antibody antigen interface prediction.Scientific reports · 2026Article
- Structural and Functional Analysis of Porcine CR1-like Proteins in C4b-Mediated Immune Responses.Veterinary sciences · 2025Article
- High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.Nature communications · 2025Article
- Increasing the fraction of correct solutions in ensembles of protein-protein docking models by an iterative consensus algorithm.Protein science : a publication of the Protein Society · 2025Article
- Article
- GRAMMCell: Docking-based Cell Modeling Resource.Journal of molecular biology · 2025Article
- Article
- Targeting GSDME-mediated macrophage polarization for enhanced antitumor immunity in hepatocellular carcinoma.Cellular & molecular immunology · 2024Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- Machine learning-assisted substrate binding pocket engineering based on structural information.Briefings in bioinformatics · 2024Article
- Synergistic acceleration of machine learning and molecular docking for prostate-specific antigen ligand design.RSC advances · 2024Article
- Pan-Cancer Analysis of PGAM1 and Its Experimental Validation in Uveal Melanoma Progression.Journal of Cancer · 2024Article
- GRAMM Web Server for Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Structure-based prediction of protein-protein interaction network in rice.Genetics and molecular biology · 2024Article
- Glycerophosphoinositol modulates FGA and NOTCH3 in exercise-induced muscle adaptation and colon cancer progression.Frontiers in pharmacology · 2024Article
- Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.Proteins · 2023Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Mutation in the D1 domain of CD4 receptor modulates the binding affinity to HIV-1 gp120.RSC advances · 2023Article
- A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling.Journal of biomedical research · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important to investigate the applicability of docking techniques to modeled proteins. We present new comprehensive benchmark sets of protein models for the development and validation of protein docking, as well as a systematic assessment of free and template-based docking techniques on these sets. As opposed to previous studies, the benchmark sets reflect the real case modeling/docking scenario where the accuracy of the models is assessed by the modeling procedure, without reference to the native structure (which would be unknown in practical applications). We also expanded the analysis to include docking of protein pairs where proteins have different structural accuracy. The results show that, in general, the template-based docking is less sensitive to the structural inaccuracies of the models than the free docking. The near-native docking poses generated by the template-based approach, typically, also have higher ranks than those produces by the free docking (although the free docking is indispensable in modeling the multiplicity of protein interactions in a crowded cellular environment). The results show that docking techniques are applicable to protein models in a broad range of modeling accuracy. The study provides clear guidelines for practical applications of docking to protein models.
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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.