ReviewProteins2013
Sampling and scoring: a marriage made in heaven.
Review in Proteins, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed.
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
- EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks.Computational and structural biotechnology journal · 2025Article
- Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics.PloS one · 2025Article
- PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries.bioRxiv : the preprint server for biology · 2023Article
- In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever.BMC medicine · 2023Article
- PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries.Bioinformatics advances · 2023Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Pushing the accuracy limit of shape complementarity for protein-protein docking.BMC bioinformatics · 2019Article
- What method to use for protein-protein docking?Current opinion in structural biology · 2019Review
- Review
- HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.Nucleic acids research · 2017Article
- New additions to the ClusPro server motivated by CAPRI.Proteins · 2017Article
- A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.Proteins · 2017Article
- Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes.Molecules (Basel, Switzerland) · 2017Review
- Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.PloS one · 2017Article
- Computing the Dynamic Supramolecular Structural Proteome.PLoS computational biology · 2017Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- Focused grid-based resampling for protein docking and mapping.Journal of computational chemistry · 2016Article
- 3DRobot: automated generation of diverse and well-packed protein structure decoys.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Most structure prediction algorithms consist of initial sampling of the conformational space, followed by rescoring and possibly refinement of a number of selected structures. Here we focus on protein docking, and show that while decoupling sampling and scoring facilitates method development, integration of the two steps can lead to substantial improvements in docking results. Since decoupling is usually achieved by generating a decoy set containing both non-native and near-native docked structures, which can be then used for scoring function construction, we first review the roles and potential pitfalls of decoys in protein-protein docking, and show that some type of decoys are better than others for method development. We then describe three case studies showing that complete decoupling of scoring from sampling is not the best choice for solving realistic docking problems. Although some of the examples are based on our own experience, the results of the CAPRI docking and scoring experiments also show that performing both sampling and scoring generally yields better results than scoring the structures generated by all predictors. Next we investigate how the selection of training and decoy sets affects the performance of the scoring functions obtained. Finally, we discuss pathways to better alignment of the two steps, and show some algorithms that achieve a certain level of integration. Although we focus on protein-protein docking, our observations most likely also apply to other conformational search problems, including protein structure prediction and the docking of small molecules to proteins.
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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.