Self-organizing superimposition algorithm for conformational sampling

被引：19

作者：

Zhu, Fangqiang ^{[1
]}

Agrafiotis, Dimitris K. ^{[1
]}

机构：

[1] Johnson & Johnson Pharmaceut Res & Dev LLC, Exton, PA 19341 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2007年 / 28卷 / 07期

关键词：

self-organizing superimposition; self-organization; self-organizing; conformational sampling; conformational analysis; distance geometry; molecular fragment; superimposition; stochastic proximity embedding;

D O I：

10.1002/jcc.20622

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

A novel self-organizing algorithm for conformational sampling is introduced, in which precomputed conformations of rigid fragments are used as templates to enforce the desired geometry. Starting from completely random coordinates, the algorithm repeatedly superimposes the templates to adjust the positions of the atoms, thereby gradually refining the conformation of the molecule. Combined with pair-wise adjustments of the atoms to resolve steric clashes, conformations that satisfy all geometric constraints can be generated from this procedure. The algorithm is demonstrated to achieve good performance and promises potential applications on more challenging modeling problems. (C) 2007 Wiley Periodicals, Inc.

引用

页码：1234 / 1239

页数：6

共 13 条

[1] *ACC SOFTW INC, 2005, CAT REL 4 10
[2] A self-organizing principle for learning nonlinear manifolds
Agrafiotis, DK
Xu, HF
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (25) : 15869 - 15872
[3] PREDICTION OF THE FOLDING OF SHORT POLYPEPTIDE SEGMENTS BY UNIFORM CONFORMATIONAL SAMPLING
BRUCCOLERI, RE
KARPLUS, M
[J]. BIOPOLYMERS, 1987, 26 (01) : 137 - 168
[4] Can we separate active from inactive conformations?
Diller, DJ
Merz, KM
[J]. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2002, 16 (02) : 105 - 112
[5] A NEW APPROACH TO PROBING CONFORMATIONAL SPACE WITH MOLECULAR MECHANICS - RANDOM INCREMENTAL PULSE SEARCH
FERGUSON, DM
RABER, DJ
[J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1989, 111 (12) : 4371 - 4378
[6] VMD: Visual molecular dynamics
Humphrey, W
Dalke, A
Schulten, K
[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) : 33 - 38
[7] A distance geometry heuristic for expanding the range of geometries sampled during conformational search
Izrailev, Serge
Zhu, Fangqiang
Agrafiotis, Dimitris K.
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2006, 27 (16) : 1962 - 1969
[8] Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations
Kirchmair, Johannes
Wolber, Gerhard
Laggner, Christian
Langer, Thierry
[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (04) : 1848 - 1861
[9] Leach A. R., 1991, REV COMPUTATIONAL CH, V2, P1
[10] THE MULTIPLE MINIMUM PROBLEM IN MOLECULAR MODELING - TREE SEARCHING INTERNAL COORDINATE CONFORMATIONAL SPACE
LIPTON, M
STILL, WC
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1988, 9 (04) : 343 - 355

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