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GRAMM v1.03
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This note is to announce the availability of GRAMM (Global RAnge
Molecular Matching) software. GRAMM is a program for protein docking. To
predict the structure of a complex, it requires only the atomic
coordinates of the two molecules (no information about the binding sites
is needed). The program performs an exhaustive 6-dimensional search
through the relative translations and rotations of the molecules. The
molecular pairs may be: two proteins, a protein and a smaller compound,
two transmembrane (TM) helices, etc. GRAMM may be used for high-
resolution molecules, for inaccurate structures (where only the gross
structural features are known), in cases of large conformational
changes, etc.
The Global Range Molecular Matching (GRAMM) methodology is an empirical
approach to smoothing the intermolecular energy function by changing the
range of the atom-atom potentials. The technique allows to locate the
area of the global minimum of intermolecular energy for structures of
different accuracy. The quality of the prediction depends on the
accuracy of the structures. Thus, the docking of high-resolution
structures with small conformational changes yields an accurate
prediction, while the docking of ultralow-resolution structures will
give only the gross features of the complex.
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I am making GRAMM publicly available following a number of requests from
different labs. I would like to make it clear, however, that both the
methodology and the program, at present, are in the process of active
development and validation, especially in the area of the low-resolution
docking, and have to be viewed like that. The program is free. However,
I would expect proper references. I will also appreciate bug reports. To
get GRAMM, send the request to ilya at guitar.rockefeller.edu. The GRAMM
site on the Web is http://guitar.rockefeller.edu/.
GRAMM was created during my stay in the Weizmann Institute (1991-1993),
in the Washington University (1993-1995), and in the Rockefeller
University (1995-1996). I deeply appreciate the assistance of my
colleagues in all these institutions (especially, Profs. Ephraim
Katchalski-Katzir, Garland Marshall, and Andrej Sali).
Platforms
Presently, GRAMM is compiled on SGI R4000, SGI R4400, SGI R8000, and SGI
R10000 Unix workstations. In the near future I will expand this list, so
check the GRAMM site for the updates. Interestingly, GRAMM also works on
a PC platform under Windows95 (the performance on P5-120 with 16 MB RAM
is only two times slower than on SGI 250 MHZ Indigo2 R4400).
Papers on GRAMM methodology
* E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A. A. Friesem, C.
Aflalo, I. A. Vakser, 1992, Molecular surface recognition:
Determination of geometric fit between proteins and their ligands by
correlation techniques, Proc. Natl. Acad. Sci. USA, 89, 2195-2199.
(Basic algorithm of protein recognition by correlation technique with
Fast Fourier transform. High-resolution 'geometric' docking).
* I. A. Vakser, C. Aflalo, 1994, Hydrophobic docking: A proposed
enhancement to molecular recognition techniques, Proteins, 20,
320-329. (High-resolution 'hydrophobic' docking).
* I. A. Vakser, G. V. Nikiforovich, 1995a, Protein docking in the
absence of detailed molecular structures, in: Methods in Protein
Structure Analysis (M. Z. Atassi & E. Appella, eds.), Plenum Press,
New York, pp. 505-514.
* I. A. Vakser, 1995b, Protein docking for low-resolution structures,
Protein Eng., 8, 371- 377. ('Low-resolution' protein docking).
* I. A. Vakser, 1996a, Long-distance potentials: An approach to the
multiple-minima problem in ligand-receptor interaction, Protein Eng.,
9, 37-41. (Interpretation of the low-resolution docking in terms of
energy potentials).
* I. A. Vakser, 1996b, Low-resolution docking: Prediction of complexes
for underdetermined structures, Biopolymers, in press (39, No.3).
(Validation of the low-resolution docking).
* I. A. Vakser, 1996c, Main-chain complementarity in protein-protein
recognition, Protein Eng., in press (9, No.7). (Docking of Ca
structures).
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Ilya A. Vakser
The Rockefeller University, Box 270
1230 York Avenue, New York, NY 10021
Phone: (212) 327-7206; Fax: (212) 327-7540
Email: ilya at guitar.rockefeller.edu
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