ArticleStructure (London, England : 1993)2016
Pushing the Backbone in Protein-Protein Docking.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching.bioRxiv : the preprint server for biology · 2025Article
- Flexible protein-protein docking with a multitrack iterative transformer.Protein science : a publication of the Protein Society · 2024Article
- Approaches to Backbone Flexibility in Protein-Protein 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
- Unveiling the affinity-stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction.Frontiers in molecular biosciences · 2023Article
- Induced fit with replica exchange improves protein complex structure prediction.PLoS computational biology · 2022Article
- IsAb: a computational protocol for antibody design.Briefings in bioinformatics · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Advances to tackle backbone flexibility in protein docking.Current opinion in structural biology · 2021Review
- Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation.Frontiers in molecular biosciences · 2021Article
- PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of chemical information and modeling · 2020Article
- Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking.Journal of chemical theory and computation · 2020Article
- Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock.Proteins · 2020Article
- Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.Proteins · 2020Article
- Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes.Structure (London, England : 1993) · 2019Article
- Refinement of protein-protein complexes in contact map space with metadynamics simulations.Proteins · 2019Article
- Efficient flexible backbone protein-protein docking for challenging targets.Bioinformatics (Oxford, England) · 2018Article
- Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.Frontiers in immunology · 2018Article
- Structure-based cross-docking analysis of antibody-antigen interactions.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Conformational changes of proteins that occur upon binding typically confound computational docking algorithms. In this study, we test computational methods to capture protein backbone conformational change related to binding. To address how well existing algorithms can sample bound-like backbones, we query seven techniques including Monte Carlo-based sampling, molecular dynamics, and normal mode analysis. All methods tested rarely sample near-bound states from the unbound conformation. Nevertheless, the direction of the predicted motions overlap with the actual conformational change. We next forced the backbone from the unbound toward the bound conformation to create a family of docking energy landscapes. Seventy percent of docking targets succeed when the unbound backbones is pushed to within 0.6 Å of the bound. Current methods can capture an average of 22% of unbound-bound transitions through conformer selection methods and another 57% through induced-fit methodologies, delineating a stubborn gap (21%) in backbone motion not covered by any current approach.
Indexed as
Identifiers
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.