ReviewCurrent opinion in structural biology2019
What method to use for protein-protein docking?
Review in Current opinion in structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
60 citing papers in PubMed, 119 citations in OpenAlex.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- The Last Mile Problem: A Critical Assessment of Physics-Based and AI Tools for Small Molecule Binding Prediction in Virtual Screening.Journal of chemical information and modeling · 2026Article
- Molecular hydrogen triggers TRPC4-TRPC4AP-dependent reversible calcium transients via extracellular influx.Theranostics · 2026Article
- Modeling Protein-Protein Complexes by Combining pyDock and AlphaFold.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Antibody Affinity Maturation by Computational Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational and experimental discovery of peptide inhibitors targeting survivin for therapeutic potential in cancer.Scientific reports · 2025Article
- A Pharmacophore-Based Method for Rapid and Accurate Virtual Screening of Antibody Libraries against Antigens.Molecular pharmaceutics · 2025Article
- A generic cross-seeding approach to protein crystallization.Journal of applied crystallography · 2025Article
- Strategies for the drug development of cancer therapeutics.Frontiers in pharmacology · 2025Review
- Predicting Epitopes of Synthetic Binding Proteins Using Protein Structure Prediction and Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics.PloS one · 2025Article
- Clinicopathological andCurrent medicinal chemistry · 2025Article
- Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes.Genomics, proteomics & bioinformatics · 2024Review
- The Art and Science of Molecular Docking.Annual review of biochemistry · 2024Review
- The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.Topics in current chemistry (Cham) · 2024Review
- Simulation and Computational Study of RING Domain Mutants of BRCA1 and Ube2k in AD/PD Pathophysiology.Molecular biotechnology · 2024Article
- Computational simulations of bispecific T cell engagers by a multiscale model.Biophysical journal · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- In silico discovery of potential PPI inhibitors for anti-lung cancer activity by targeting the CCND1-CDK4 complex via the P21 inhibition mechanism.Frontiers in chemistry · 2024Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
A number of well-established servers perform 'free' docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. On the basis of the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. In accordance with the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.
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What OpenQuestion holds
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.