| General
Literature in Structural Bioinformatics |
- Holm, L. and Sander, C. 1996. Mapping the protein universe.
Science 273:595-602.
|
| Protein Ligand Docking |
- Softwares :
- GOLD
:
Genetic Optimization
for Ligand Docking. It is a genetic algorithms based program for
docking
ligand into proteins. It allows full ligand flexibility and
partial
protein flexibility. The references are:
- Gareth Jones, Peter Willett, Robert C. Glen, Andrew R.
Leach and Robin
Taylor(1997). Development and Validation of a Genetic Algorithm for
Flexible
Docking, Journal of Molecular Biology 267, 727-748.
- FlexX
:
- Rarey, M., Kramer, B., Lengauer, T. & Klebe, G.
(1996). A Fast
Flexible
Docking Method using an Incremental Construction Algorithm. Journal of
Molecular Biology 261(3), 470-489.
- Dock : A
Fast
docking program
developed by the Kuntz
group at Molecular Design Institute,
University of California at
San Fransisco.
References :
- Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R.,
and T.E.
Ferrin,
"A geometric approach to macromolecule-ligand interactions", J. Mol.
Biol.
161, 269-288 (1982) .
|
| Protein Structure Classification |
- Resources :
- SCOP : This is a
manually prepared structure based classification of proteins.
|
| Protein Structure Alignment |
- Softwares :
- DALI : This is a
method of structural alignment based on distance matrix represnetation.
It aligns hexapeptides, and uses Monte Carlo Optimization to build the
alignment. This service is available for free.
- Holm, L. and Sander, C. 1993. Protein structure
comparison by alignment of distance matrices. Journal of Molecular
Biology 233: 123-138.
- Holm, L. and Sander, C. 1996. The FSSP database: fold
classification based on structure-structure alignment of proteins.
Nucleic Acids Research 24(1):206-209.
- Holm, L. and Sander, C. 1996. Mapping the protein
universe. Science 273:595-602.
- Combinatorial
Extension : A fast structural alignment method based on extension
of matches through the sequences of the 2 matching proteins.
- VAST :
Vector Alignment Search Tool.
- Gibrat JF, Madej T, Bryant SH. Surprising
similarities in structure comparison. Curr Opin Struct Biol 1996
Jun; 6(3):377-385.
- Madej T, Gibrat JF, Bryant SH. (1995) Threading a
database of protein cores. Proteins 1995 Nov; 23(3):356-3690.
- LOCK : A
vector based iterative structure alignment tool which uses secondary
structure vectors.
- Shapiro, J.C. and Brutlag, D.L. (2004). FoldMiner:
Structural Motif Discovery Using an Improved Superposition Algorithm
Protein Science 13(1) 278-294.
- Singh, A.P. and Brutlag, D.L. (1997). Hierarchical
Protein Structure Superposition using both Secondary Structure and
Atomic Representations. Proc. Intelligent Systems for Molecular Biology
5:284-293.
- Flexprot
: A flexible structure comparison program which uses hinges to provide
flexibility.
- "Flexible protein alignment and hinge detection", M.
Shatsky, H.J. Wolfson, and R. Nussinov, Proteins: Structure, Function,
and Genetics 48:242-256, 2002.
|