In recent years, a variety of approaches have been developed for ‘protein–peptide docking’, that is, predicting the structure of the protein–peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and...
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the ...
Highly flexible protein-peptide docking using CABS-dock, URL http://arxiv.org/abs/1605.09303 (2016).M. P. Ciemny, M. Kurcinski, K. J. Kozak, A. Kolinski, and S. Kmiecik, "Highly flexible protein-peptide docking using CABS- dock," in Modeling Peptide-Protein Interactions, vol. 1561 ...
Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in HADDOCK score in the context of protein-peptide docking simulations. 展开 关键词: MM-PBSA scoring function binding free energies haddock protein-peptide interaction ...
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...
bioinformaticschemistrystructural-biologymolecular-structuresprotein-structureartificial-intelligencednaproteinproteomicsdockingpeptidesmolecular-biologyprotein-designprotein-protein-interactionswarm-intelligencestructural-bioinformaticsprotein-dna-interactionsbioinformatics-toolglowworm-swarm-optimizationprotein-docking ...
A flexible protein−peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexi...
protein–peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a ...
同时定义了一个区分天然结合构象和非天然结合构象的筛选参数.用上述方法预测多肽–蛋白质的结合构象,结果显示该方法能成功预测蛋白质的结合位点,且多数多肽的预测构象的Cα-RMSD在5.5 A以下.因此,研究结果表明,所发展的方法在蛋白质多肽结合位点预测方面有很好的应用价值.Protein-peptidebinding plays various important ...
We additionally compared CAMP with other methods on several representative benchmark data sets (Supplementary Table4) that were originally used to evaluate the performance of peptide docking and detecting “hotspots” at protein interface34,39,40,41,42. As shown in Supplementary Fig.9, CAMP still ...