GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization Nucleic Acids Res., 43 (2015), pp. W431-W435 CrossrefView in ScopusGoogle Scholar 20 M.F. Lensink, et al. Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition Proteins...
published for other small-molecule docking programs (AutoDockVina benchmark and LEADSPEP), the performance of rDock could directly be compared to the performances of AutoDockVina, Surflex, GOLD, and Glide, as well as to the peptide docking protocol PIPER-FlexPepDock and...
Results: Here we present AutoDock CrankPep or ADCP in short, a novel approach to dock flexible peptides into rigid receptors. ADCP folds a peptide in the potential field created by the protein to predict the protein-peptide complex. We show that it outperforms leading peptide docking methods ...
Firedock gives the 10 best-refined docking solutions of protein and peptide based on global energy. protein and peptide docking results from Firdock were visualized by UCSF chimaera. The results show that the predicted 3D structure has two binding domains. The String database observed protein-...
There are various docking methods to study peptide–protein complexes. Majorly, these methods can be divided into three groups: peptide–protein docking, protein–protein docking, and protein–ligand docking. Among them, peptide–protein docking has specifically been developed to dock peptides on then...
i.e. it predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. The AutoDockSuite consists of two main programs of which AutoDock performs the docking of the ligand to a set of grids describing the target protein and AutoGrid pre-calc...
About Protein-ligand docking code autodock vina from vina.scripps.edu License Apache-2.0 license Activity Stars 6 stars Watchers 2 watching Forks 5 forks Report repository Releases No releases published Packages No packages published Languages C++ 65.0% C 35.0% Footer...
PEX5-PEX14 PPI is mediated by the WxxxF/Y peptide motifs of the canonical α-helix of PEX5, with the indole and phenyl ring systems of Trp i and Phe i+4 residues located on the same face of the helix [7]. These aromatic moieties fill the respective Trp and Phe hot-spots in the...
4.2.1. Protein–Ligand Docking 分子对接是一种广泛使用的、相对快速和经济的计算工具,用于在计算中预测分子识别事件的结合方式和亲和力[14]。蛋白质-配体对接是分子对接领域的一个分支,由于在当前药物发现过程中的重要性,它代表了一种特别重要的方法,即在大规模的可用化学物质数据库中进行虚拟筛选,以选择可能的药物...
Vengadesan K, Gautham N (2004) An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides. Biochem Biophys Res Commun 316:731–737 Article CAS Google Scholar Prasad PA, Gautham N (2008) A new peptide docking strategy using a mean field...