Gaussian docking functions

Biopolymers - Tập 68 Số 1 - Trang 76-90 - 2003
Mark McGann1, Harold R. Almond2, Anthony Nicholls1, Jennifer Grant3, Frank J. Schoenen4
1Open Eye Scientific Software, Santa Fe, NM 87501, USA.
2Johnson & Johnson Pharmaceutical Research and Development LLC, Springhouse, PA 19477, USA
3Astra Zeneca Pharmaceuticals, EST(Chem) 26F17, Mereside, Macclesfield, Cheshire, SK10 4TG UK
4Johnson & Johnson Pharmaceutical Research and Development, LCC, 1000 Route 202, Raritan, NJ 08869

Tóm tắt

AbstractA shape‐based Gaussian docking function is constructed which uses Gaussian functions to represent the shapes of individual atoms. A set of 20 trypsin ligand–protein complexes are drawn from the Protein Data Bank (PDB), the ligands are separated from the proteins, and then are docked back into the active sites using numerical optimization of this function. It is found that by employing this docking function, quasi‐Newton optimization is capable of moving ligands great distances [on average 7 Å root mean square distance (RMSD)] to locate the correctly docked structure. It is also found that a ligand drawn from one PDB file can be docked into a trypsin structure drawn from any of the trypsin PDB files. This implies that this scoring function is not limited to more accurate x‐ray structures, as is the case for many of the conventional docking methods, but could be extended to homology models. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 76–90, 2003

Từ khóa


Tài liệu tham khảo

10.1126/science.257.5073.1078

10.1093/protein/7.3.385

10.1021/cr00023a004

Böhm H. J., 1994, J Comput‐Aided Mol Design, 8, 243, 10.1007/BF00126743

10.1016/1074-5521(95)90050-0

10.1021/jm990352k

10.1021/jm0003992

10.1023/A:1008068903544

10.1073/pnas.93.17.8945

10.1007/s002140050420

10.1002/(SICI)1096-987X(199912)20:16<1740::AID-JCC6>3.0.CO;2-A

10.1023/A:1011115820450

10.1002/prot.340080302

10.1007/BF00402820

10.1016/S0022-2836(95)80037-9

Judson R. S.;Jaeger E. P.;Treasurywala A. M.Sandia National Laboriatories1993 SAND93‐8688.

10.1007/BF00124402

10.1016/0263-7855(93)87001-L

10.1006/jmbi.1996.0477

10.1002/jcc.540130608

10.1016/S1074-5521(96)90093-9

10.1007/BF00119865

10.1016/0022-2836(91)90859-5

10.1002/(SICI)1097-0134(199607)25:3<342::AID-PROT6>3.0.CO;2-H

10.1021/ar00041a001

10.1002/jcc.540130311

10.1021/j100011a016

10.1007/978-94-017-1120-3_5

10.1016/S0022-2836(77)80200-3

Thông tin
Thông tin xuất bản

Biopolymers

Tập 68 Số 1

76-90

Thông tin tác giả