ArticleBMC bioinformatics2011
ASPDock: protein-protein docking algorithm using atomic solvation parameters model.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- A computational model of ESAT-6 complex in membrane.Journal of theoretical & computational chemistry · 2020Article
- StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions.Frontiers in molecular biosciences · 2020Article
- Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery.Molecules (Basel, Switzerland) · 2018Review
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.Journal of computational chemistry · 2017Article
- Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.Scientific reports · 2016Article
- Applying Side-chain Flexibility in Motifs for Protein Docking.Genomics insights · 2015Article
- IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.BMC bioinformatics · 2014Article
- Article
- DOT2: Macromolecular docking with improved biophysical models.Journal of computational chemistry · 2013Article
- Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.Journal of proteome research · 2013Article
- A novel protocol for three-dimensional structure prediction of RNA-protein complexes.Scientific reports · 2013Article
- How to use not-always-reliable binding site information in protein-protein docking prediction.PloS one · 2013Article
- Prediction of functionally important residues in globular proteins from unusual central distances of amino acids.BMC structural biology · 2011Article
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5 authors.
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Abstract
backgroundAtomic Solvation Parameters (ASP) model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock).
resultsThe ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69) with the binding free energies than the pure shape complementarity scores (r ≈ 0.48). The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19.
conclusionsASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.
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