Resources :: GRAMM v1.03
Global Range Molecular Matching
Protein-Protein Docking and Protein-Ligand Docking
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 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 locates 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. More information about the GRAMM methodology is on our laboratory research page.
GRAMM was made publicly available following a number of requests from different labs. We would like to make it clear, however, that both the methodology and the program, at present, are in the process of active development, and have to be viewed like that. The program is free. However, we would expect proper references. Bug reports will be also appreciated.
GRAMM is compiled on SGI R10000, SGI R4000, SGI R4400, SGI R8000, Sun SPARC, IBM RS6000, DECAlpha, and PC (Windows and Linux). Windows version must work on all 32-bit flavors of the MS Windows operating system. Linux version was compiled on RedHat with glibc2.0.
Basic papers on GRAMM methodology
- Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 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).
- Vakser, I.A., Aflalo, C., 1994, Hydrophobic docking: A proposed enhancement to molecular recognition techniques, Proteins , 20:320-329. (High-resolution hydrophobic docking).
- Vakser, I.A., Nikiforovich, G.V., 1995, Protein docking in the absence of detailed molecular structures, in: Methods in Protein StructureAnalysis (M. Z. Atassi & E. Appella, eds.), Plenum Press, New York, pp. 505-514.
- Vakser, I.A., 1995, Protein docking for low-resolution structures, Protein Eng., 8:371- 377. (Low-resolution protein docking).
- Vakser, I.A., 1996, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9:37-41. (Interpretation of low-resolution docking in terms of energy potentials).
- Vakser, I.A., 1996, Low-resolution docking: Prediction of complexes for underdetermined structures, Biopolymers , 39:455-464. (Validation of low-resolution docking) .
- Vakser, I.A., 1996, Main-chain complementarity in protein-protein recognition, Protein Eng., 9:741-744. (Docking of C-alpha structures).
- Vakser, I.A., 1997, Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex, Proteins , Suppl.1:226-230. (GRAMM performance at CASP) .
- Vakser, I.A., Matar, O.G., Lam, C.F., 1999, A systematic study of low-resolution recognition in protein-protein complexes, Proc. Natl. Acad. Sci. USA, 96:8477-8482. (Large scale low-resolution docking).