ArticleProteins2010
FiberDock: Flexible induced-fit backbone refinement in molecular docking.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 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
76 citing papers in PubMed.
- Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning.Biomolecules · 2025Review
- Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis.Interdisciplinary sciences, computational life sciences · 2023Article
- Gibbs Energy and Gene Expression Combined as a New Technique for Selecting Drug Targets for Inhibiting Specific Protein-Protein Interactions.International journal of molecular sciences · 2023Article
- Towards universal synthetic heterotrophy using a metabolic coordinator.Metabolic engineering · 2023Article
- The structural principles underlying molybdenum insertase complex assembly.Protein science : a publication of the Protein Society · 2023Article
- Molecular Cloning, Expression, Sequence Characterization and Structural Insight of Bubalus bubalis Growth Hormone-Receptor.Molecular biotechnology · 2023Article
- Local Normal Mode Analysis for Fast Loop Conformational Sampling.Journal of chemical information and modeling · 2022Article
- Induced fit with replica exchange improves protein complex structure prediction.PLoS computational biology · 2022Article
- Article
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Memdock: An α-Helical Membrane Protein Docking Algorithm.Methods in molecular biology (Clifton, N.J.) · 2021Article
- PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of chemical information and modeling · 2020Article
- Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation.Molecular genetics & genomic medicine · 2020Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock.Proteins · 2020Article
- Predicting Protein Functional Motions: an Old Recipe with a New Twist.Biophysical journal · 2020Article
- Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Upon binding, proteins undergo conformational changes. These changes often prevent rigid-body docking methods from predicting the 3D structure of a complex from the unbound conformations of its proteins. Handling protein backbone flexibility is a major challenge for docking methodologies, as backbone flexibility adds a huge number of degrees of freedom to the search space, and therefore considerably increases the running time of docking algorithms. Normal mode analysis permits description of protein flexibility as a linear combination of discrete movements (modes). Low-frequency modes usually describe the large-scale conformational changes of the protein. Therefore, many docking methods model backbone flexibility by using only few modes, which have the lowest frequencies. However, studies show that due to molecular interactions, many proteins also undergo local and small-scale conformational changes, which are described by high-frequency normal modes. Here we present a new method, FiberDock, for docking refinement which models backbone flexibility by an unlimited number of normal modes. The method iteratively minimizes the structure of the flexible protein along the most relevant modes. The relevance of a mode is calculated according to the correlation between the chemical forces, applied on each atom, and the translation vector of each atom, according to the normal mode. The results show that the method successfully models backbone movements that occur during molecular interactions and considerably improves the accuracy and the ranking of rigid-docking models of protein-protein complexes. A web server for the FiberDock method is available at: http://bioinfo3d.cs.tau.ac.il/FiberDock.
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.