ReviewCurrent opinion in structural biology2021
Advances to tackle backbone flexibility in protein docking.
Review in Current opinion in structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The mechanism of probiotics in pregnancy outcomes in overweight or obese pregnant women based on meta-analysis, network pharmacology and molecular docking.BMC pregnancy and childbirth · 2025Pooled it
- Simulation of cell-size systems at long timescales with flexible protein structures.bioRxiv : the preprint server for biology · 2026Article
- Review
- Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching.bioRxiv : the preprint server for biology · 2025Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Review
- Structure-Based Identification of Non-covalent Prolyl Oligopeptidase 80 Inhibitors TargetingJournal of chemical information and modeling · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta.Journal of chemical theory and computation · 2024Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.bioRxiv : the preprint server for biology · 2024Article
- Approaches to Backbone Flexibility in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Molecular Dynamics and Other HPC Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Docking Foundations: From Rigid to Flexible Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.Bioinformatics advances · 2023Article
- How to Design Peptides.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants.Computational biology and chemistry · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were submitted in less than 20% of the 'difficult' targets (with significant backbone change or uncertainty). Here, we describe recent developments in protein-protein docking and highlight advances that tackle backbone flexibility. In molecular dynamics and Monte Carlo approaches, enhanced sampling techniques have reduced time-scale limitations. Internal coordinate formulations can now capture realistic motions of monomers and complexes using harmonic dynamics. And machine learning approaches adaptively guide docking trajectories or generate novel binding site predictions from deep neural networks trained on protein interfaces. These tools poise the field to break through the longstanding challenge of correctly predicting complex structures with significant conformational change.
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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.