منابع مشابه
Binding Pocket Optimization by Computational Protein Design
Engineering specific interactions between proteins and small molecules is extremely useful for biological studies, as these interactions are essential for molecular recognition. Furthermore, many biotechnological applications are made possible by such an engineering approach, ranging from biosensors to the design of custom enzyme catalysts. Here, we present a novel method for the computational ...
متن کاملEpock: rapid analysis of protein pocket dynamics
SUMMARY The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a g...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملProbing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.
Based on the elastic network model, we develop a new analysis for protein complexes, which probes the local dynamics of a subsystem that is elastically coupled to a fluctuating environment. This method is applied to a comparative dynamical analysis of the nucleotide-binding pocket of two motor proteins-myosins and kinesins. In myosins, the observed structural changes in the nucleotide-pocket fr...
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ژورنال
عنوان ژورنال: Accounts of Chemical Research
سال: 2016
ISSN: 0001-4842,1520-4898
DOI: 10.1021/acs.accounts.5b00516