dorsal/arxiv
View SchemaPIPER: An FFT-based Protein Docking Program with Pairwise Potentials
| Authors | D. Kozakov, R. Brenke, S. Comeau, S. Vajda |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0605018 |
| URL | https://arxiv.org/abs/q-bio/0605018 |
Abstract
The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this restriction is removed, and the approach is efficiently used with pairwise interactions potentials that substantially improve the docking results. The basic idea is approximating the interaction matrix by its eigenvectors corresponding to the few dominant eigenvalues, resulting in an energy expression written as the sum of a few correlation functions, and solving the problem by repeated FFT calculations. In addition to describing how the method is implemented, we present a novel class of structure based pairwise intermolecular potentials. The DARS (Decoys As the Reference State) potentials are extracted from structures of protein-protein complexes and use large sets of docked conformations as decoys to derive atom pair distributions in the reference state. The current version of the DARS potential works well for enzyme-inhibitor complexes. With the new FFT-based program, DARS provides much better docking results than the earlier approaches, in many cases generating 50\% more near-native docked conformations. Although the potential is far from optimal for antibody-antigen pairs, the results are still slightly better than those given by an earlier FFT method. The docking program PIPER is freely available for non-commercial applications.
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"abstract": "The Fast Fourier Transform (FFT) correlation approach to protein-protein\ndocking can evaluate the energies of billions of docked conformations on a grid\nif the energy is described in the form of a correlation function. Here, this\nrestriction is removed, and the approach is efficiently used with pairwise\ninteractions potentials that substantially improve the docking results. The\nbasic idea is approximating the interaction matrix by its eigenvectors\ncorresponding to the few dominant eigenvalues, resulting in an energy\nexpression written as the sum of a few correlation functions, and solving the\nproblem by repeated FFT calculations. In addition to describing how the method\nis implemented, we present a novel class of structure based pairwise\nintermolecular potentials. The DARS (Decoys As the Reference State) potentials\nare extracted from structures of protein-protein complexes and use large sets\nof docked conformations as decoys to derive atom pair distributions in the\nreference state. The current version of the DARS potential works well for\nenzyme-inhibitor complexes. With the new FFT-based program, DARS provides much\nbetter docking results than the earlier approaches, in many cases generating\n50\\% more near-native docked conformations. Although the potential is far from\noptimal for antibody-antigen pairs, the results are still slightly better than\nthose given by an earlier FFT method. The docking program PIPER is freely\navailable for non-commercial applications.",
"arxiv_id": "q-bio/0605018",
"authors": [
"D. Kozakov",
"R. Brenke",
"S. Comeau",
"S. Vajda"
],
"categories": [
"q-bio.BM"
],
"title": "PIPER: An FFT-based Protein Docking Program with Pairwise Potentials",
"url": "https://arxiv.org/abs/q-bio/0605018"
},
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