Patent
Ligand search device, ligand search method, program and recording medium
Umeyama Hideaki,Watanabe Yoshiaki,Arai Ryoichi +2 more
- 14 Mar 2005
4
TL;DR: In this paper, a ligand search device for studying the analysis of acceptor/ligand binding including even an induced fit type acceptor was provided, where the acceptor's normal vibration analysis was performed first, and the fluctuation of the main chain dihedral angle was calculated.
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Abstract: PROBLEM TO BE SOLVED: To provide a ligand search device for studying the analysis of acceptor/ligand binding including even an induced fit type acceptor, a ligand search method, a program and a recording medium. SOLUTION: The normal vibration analysis calculation of the acceptor is performed first, and the fluctuation of the main chain dihedral angle of the acceptor in a steady state is calculated. Then, by performing molecular dynamics calculation while applying constraints based on the fluctuation to each atom, the more accurate dynamic structure of the acceptor is predicted. Also, by using the dynamic structure obtained by the molecular dynamics calculation and an interaction function, the acceptor/ligand binding applicable even to the induced fit type acceptor is accurately predicted. COPYRIGHT: (C)2006,JPO&NCIPI
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Citations
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TL;DR: In this paper, a multi-modal protein conformational space optimization method based on composite structure features was proposed, which comprises the following steps that: on the basis of an evolutionary algorithm framework, RosettaScore3 is taken as an optimized objective function, and statistics is carried out to obtain three types of structure features, including the individual distance spectrum, the individual secondary structure spectrum and the individual dihedral angle spectrum of a population individual.
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TL;DR: In this paper, the anchor point of a target molecule is determined by using atoms having small fluctuation in the target molecule existing within the range of 5Å to 15 Å from an anchor point with the center of gravity of the pharmaceutical candidate molecule as the anchor points.
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Device for predicting change in interaction force and method for predicting change in interaction force
Noriko Shimba,榛葉 教子 +1 more
- 16 Aug 2010
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