Subject: Summary: Protein Docking

From: Danilo Gonzalez <[email-masked]>
Date: Wed, 06 Dec 2000 11:19:14 -0300

Dear CCLers,

Thanks  Sohail, Michael Meyer, and Richard Gillilan  for their excelente
response.  Thank you very much.

My previous question is:
---------------------------------------------------------------------------

I'm looking for some references about the protein docking and
interaction
between proteins. I will appreciate if you can send me some references
about this subject.
--------------------------------------------------------------------------

I summarizes all the responses as follows,

********************************************************
  Have a look at this site.

     http://www.scripps.edu/pub/olson-web/doc/autodock/references.html

In addition subscribe to chemwem.Its a dreat collection of refrences.
  http://www.chemweb.com

what method u will use for docking might be I can give u some more
information.

sohail
university sains malaysia.

***********************************************************
Dear Fernando,

here are a few  references. There are  a lot of other interesting
references cited
in these papers.

N. Horton, M. Lewis, Calculation of the free energy of association for
protein
complexes,
    Protein Sci. 1, 169 (1992).
J. Janin, Elusive Affinities, Proteins 21, 30 (1995).
J. Janin, Principles of Protein-protein recognition - from structure to
thermodynamics,
    Biochimie 77, 497 (1995)
J. Janin, F. Rodier, Protein-Protein interaction at crystal contacts,
Proteins 23,
580 (1995).
D. Fischer et al., A geometry-bases suite of molecular docking
processes, JMB 248,
459 (1995).
C.-J. Tsai et al., Protein-Protein interfaces: ..., Critical rev.
Biochem. Mol.
Bio. 3, 127 (1996).
M. Meyer et al., Hydrogen bonding and molecular surface shape
complementarity ...,
JMB 264, 199 (1996).
J. Otlewski, W. Apostoluk, Structural and energetical aspects of
protein-protein
recognition, Acta
    Biochimica Polonica 44, 367 (1997).
N. S. Blohm, J. Sygusch, High resolution fast quantitative docking using
Fourie
Domain correlation
    techniques, Proteins 27, 493 (1997).
R. M. Jackson et al., Rapid refinement if protein interfaces
incorporating
solvation:..., KMB 276, 265 (1998).
M. J. E. Sternberg et al., Predictive docking of protein-protein and
protein-DNA
complexes, Curr. Opin.
    Struct. Biol. 8, 250 (1998).

Michael
--
Michael Meyer
Konrad-Zuse-Zentrum
Takustrasse 7
D-14195 Berlin
Germany

E-mail: [email-masked]
Tel. (++49) 30/84185-327
Fax  (++49) 30/84185-107
http://www.zib.de/meyer/

**********************************************************

Protein-protein interaction:

J.A. McCammon "Theory of biomolecular recognition"
Curr. Op. in Struct Biol. 1998 8:245-249

S. Jones and J. M. Thornton "Principles of protein-protein interaction"
Proc. Natl. Acad. Sci. USA vol 93 pp 13-20 Jn 1996

J. Janin and C. Chothia "The Structure of Protein-Protein Recognition
Sites"
J. Biol. Chem vol 265 no 27 pp 16027-16030 1990

J. Janin, S Miller, C Cothia "Surface, Subunit Interfaces and Interior
of Oligomeric Proteins"
J. Mol Bio. (1988) 204 pp155-164

Docking:

J. Cherfils and J. Janin "Protein docking algorithms: simulating
molecular recognition"
Current Opinion in Structural Biology 1993, 3:265-269

M. Sternberg, H.A. Gbb ad RM Jackson "Protein docking algorithms:
simulating molecular
recognition" Current opinion in Structural Biology 1998, 8:250-256

I. A. Vakser, O. G. Matar and C. F. Lam "A Systematic Study of
low-resolution recognition in
protein-protein complexes" PNAS vol 96 pp8477-8482 1999

D. Fischer et.al. "A Geometry-based Suite of Molecular Docking
Processes"
J. Mol. Bio. (1995) 248 pp459-477

FTDOCK (Gabb J. Mol Biol 272 106-120 1997)

DOT (Lynn F. Ten Eyck) sorry don't have a ref for this program

Also check out Bruce Duncan's Harmony program:
http://www.scripps.edu/pub/olson-web/doc/harmony/harmony.html

Hope this helps.

Richard Gillilan
MacCHESS/MBG
Cornell University