ArticlePloS one2013
Protein-protein docking with F(2)Dock 2.0 and GB-rerank.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A comprehensive survey of scoring functions for protein docking models.BMC bioinformatics · 2025Article
- Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking.Journal of chemical information and modeling · 2023Article
- Paraquat is an agonist of STIM1 and increases intracellular calcium levels.Communications biology · 2022Article
- Computational Study of Natural Compounds for the Clearance of Amyloid-Βeta: A Potential Therapeutic Management Strategy for Alzheimer's Disease.Molecules (Basel, Switzerland) · 2019Article
- Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy.Biochemistry · 2019Article
- GPU-based detection of protein cavities using Gaussian surfaces.BMC bioinformatics · 2017Article
- IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.Bioinformatics (Oxford, England) · 2017Article
- Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2016Article
- X-ray, Cryo-EM, and computationally predicted protein structures used in integrative modeling of HIV Env glycoprotein gp120 in complex with CD4 and 17b.Data in brief · 2016Article
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.Biophysical journal · 2016Article
- Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.Structure (London, England : 1993) · 2015Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
- IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.BMC bioinformatics · 2014Article
- NONUNIFORM FOURIER TRANSFORMS FOR RIGID-BODY AND MULTI-DIMENSIONAL ROTATIONAL CORRELATIONS.SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics · 2013Article
- Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
7 authors.
Funding
Abstract
motivationComputational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F(2) Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA) based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error.
resultsThe improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F(2) Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F(2) Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F(2) Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F(2) Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other. AVAILABILITY: The docking protocol has been implemented as a server with a graphical client (TexMol) which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server: http://www.cs.utexas.edu/~bajaj/cvc/software/f2dock.shtml. Client: http://www.cs.utexas.edu/~bajaj/cvc/software/f2dockclient.shtml.
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