A computational system for modelling flexible protein-protein and protein-DNA docking.
A computational system is described that predicts the structure of protein/protein and protein/DNA complexes starting from unbound coordinate sets. The approach is (i) a global search with rigid-body docking for complexes with shape complementarity and favourable electrostatics; (ii) use of distance constraints from experimental (or predicted) knowledge of critical residues; (iii) use of pair potential to screen docked complexes and (iv) refinement and further screening by protein-side chain optimisation and interfacial energy minimisation. The system has been applied to model ten protein/protein and eight protein-repressor/DNA (steps i to iii only) complexes. In general a few complexes, one of which is close to the true structure, can be generated.
Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, UK. m.sternberg@icrf.icnet.uk
M J
MJ
Sternberg
P
P
Aloy
H A
HA
Gabb
R M
RM
Jackson
G
G
Moont
E
E
Querol
F X
FX
Aviles
D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D005583:Fourier Analysis; D046911:Macromolecular Substances; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012097:Repressor Proteins / Q000737:chemistry; D012997:Solvents; D013816:Thermodynamics
D046911:Macromolecular Substances; D011506:Proteins; D012097:Repressor Proteins; D012997:Solvents; D004247:DNA