Molecular disassembly with RRT-like algorithms

被引:24
作者
Cortes, Juan [1 ]
Jaillet, Leonard [1 ]
Simeon, Thierry [1 ]
机构
[1] CNRS, LAAS, 7 Ave Colonel Roche, F-31077 Toulouse, France
来源
PROCEEDINGS OF THE 2007 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION, VOLS 1-10 | 2007年
关键词
D O I
10.1109/ROBOT.2007.363982
中图分类号
TP [自动化技术、计算机技术];
学科分类号
0812 ;
摘要
This paper addresses the problem of computing pathways for a ligand to exit from the active site of a protein. Such problem can be formulated as a mechanical disassembly problem for two articulated objects. Its solution requires searching paths in a constrained high-dimensional configuration-space. Indeed, the ligand passageway inside the protein is often extremely cluttered so that current path planning techniques are unable to solve the disassembly problem in reasonable computing time. The techniques presented in this paper are based on the RRT algorithm. First we discuss some simple and general modifications of the basic algorithm that significantly improve its performance. Then we describe a new variant of the planner that treats ligand and protein degrees of freedom separately. This new algorithm outperforms the basic RRT, particularly for very constrained problems, and is able to handle models with hundreds of degrees of freedom. We analyze the effects of each RRT variant via several examples of different complexity. Although discussions and results of this paper focus on molecular models, the ideas behind the algorithms are general and can be applied to path planners for disassembling articulated mechanical parts.
引用
收藏
页码:3301 / +
页数:2
相关论文
共 27 条
[1]   Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures [J].
Amato, NM ;
Dill, KA ;
Song, G .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2003, 10 (3-4) :239-255
[2]   Choosing good distance metrics and local planners for probabilistic roadmap methods [J].
Amato, NM ;
Bayazit, OB ;
Dale, LK ;
Jones, C ;
Vallejo, D .
IEEE TRANSACTIONS ON ROBOTICS AND AUTOMATION, 2000, 16 (04) :442-447
[3]   Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion [J].
Apaydin, MS ;
Brutlag, DL ;
Guestrin, C ;
Hsu, D ;
Latombe, JC ;
Varma, C .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2003, 10 (3-4) :257-281
[4]  
Bohm H.-J., 2006, PROTEIN LIGAND INTER, V19
[5]  
Cheng P, 2001, IROS 2001: PROCEEDINGS OF THE 2001 IEEE/RJS INTERNATIONAL CONFERENCE ON INTELLIGENT ROBOTS AND SYSTEMS, VOLS 1-4, P43, DOI 10.1109/IROS.2001.973334
[6]   A path planning approach for computing large-amplitude motions of flexible molecules [J].
Cortés, J ;
Siméon, T ;
de Angulo, VR ;
Guieysse, AD ;
Remaud-Siméon, M ;
Tran, V .
BIOINFORMATICS, 2005, 21 :I116-I125
[7]   Geometric algorithms for the conformational analysis of long protein loops [J].
Cortés, J ;
Siméon, T ;
Remaud-Siméon, M ;
Tran, V .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (07) :956-967
[8]  
CORTES J, 2007, UNPUB IFAC WORKSH IN
[9]  
DEANGULO VR, 2005, ROBOTICS SCI SYSTEMS, P6
[10]   Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles [J].
DePristo, MA ;
de Bakker, PIW ;
Lovell, SC ;
Blundell, TL .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 51 (01) :41-55