Name
Abstract | ||
|---|---|---|
A new method for considering solvation when calculating electrostatics for protein docking is proposed. The solvent-exposed charges are attenuated by induced solvent polarization charges. Modified charges are pre-calculated and the correction doesn't affect the speed of the actual simulation. The new Screened Charge Electrostatic Model (SChEM) results in an improved discrimination of near-native solutions from false positives in docking simulations as compared to conventional 'non-solvated' charge assignment. A series of protein-protein complexes were analyzed by running automated rigid-body Monte-Carlo docking simulations using the 3-D coordinates of the unbound components. In all but one case, the use of solvation screened charges for electrostatic calculations helped to improve the rank of the near-native solution after rigid-body simulations. The SChEM also drastically improved the results of the subsequent refinement of the interface side-chains. In all cases the final lowest energy solution was found within 3.0 A r.m.s.d. of the crystal structure. |
Year | Venue | Keywords |
|---|---|---|
2002 | Pacific Symposium on Biocomputing | complex network,protein protein interaction,rigid body,protein complex,mathematical model |
Field | DocType | ISSN |
Electrostatics,Chemical physics,Biology,Docking (dog),Protein protein,Crystal structure,Solvation,Genetics | Conference | 2335-6936 |
Citations | PageRank | References |
0 | 0.34 | 1 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Juan Fernandez-Recio | 1 | 1 | 1.04 |
| Maxim Totrov | 2 | 269 | 31.59 |
| Ruben Abagyan | 3 | 430 | 55.44 |