【摘 要】
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We have developed a software package PPSPT (Peptide and Protein Structure Prediction Toolkit) to predict the energetically stable structures of peptide and prot
【机 构】
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HefeiNationalLaboratoryforPhysicalSciencesatMicroscale,DepartmentofPhysics,UniversityofScienceandTec
【出 处】
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8th IUPAP International Conference on Biological Physics(第八届
论文部分内容阅读
We have developed a software package PPSPT (Peptide and Protein Structure Prediction Toolkit) to predict the energetically stable structures of peptide and protein.This suit offers a workflow which can easily process continuouslythe steps involved in a structure prediction method.The suit also allows for combiningcomputational steps among different methods.The structure prediction methods implemented presently include a systematic search algorithm, a Monte Carlo sampling method anda particle-swarm optimization algorithm.Each search method may involve a number of computational steps.For example, a systematic search of the potential energy surface of polypeptide starts with generating trialstructures by considering all combinations of the molecular bond rotational degrees of freedom, followed by a semi-empirical and ab initio combined determination of the stable conformers.These steps are seamlessly integrated in the toolkit.Thetoolkit consists of a distribution calculation system written in Python, a structure generator, a database, a data analyst suit, and several other research programs.
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