Accurate general method for lattice approximation of three-dimensional structure of a chain molecule.
An algorithm based on dynamic programming gives the lattice models having the minimal RMS deviations from the actual folds of protein (RNA, etc.) chains for a given lattice and a given orientation of the macromolecule relative to the lattice. The algorithm is applicable for 3-D lattices of any kind. The accuracy of the lattice approximation increases when the distance between neighbor chain links is not rigidly fixed. Special repulsive potentials facilitate generation of self-avoiding lattice chains. The results of model building show the efficiency and precision of this proposed general method when compared with others.
Rykunov
D S
DS
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region.
Reva
B A
BA
Finkelstein
A V
AV
D000465:Algorithms; D007611:Aprotinin / Q000737:chemistry; D001536:Bence Jones Protein / Q000737:chemistry; D003198:Computer Simulation; D003459:Crystallins / Q000737:chemistry; D003574:Cytochrome c Group / Q000737:chemistry; D005288:Ferredoxins / Q000737:chemistry; D005418:Flavodoxin / Q000737:chemistry; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D008958:Models, Molecular; D008961:Models, Structural; D009690:Nucleic Acid Conformation; D010320:Parvalbumins / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D010970:Plastocyanin / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D012313:RNA / Q000737:chemistry*; D012360:RNA, Transfer, Phe / Q000737:chemistry; D012259:Ribonuclease, Pancreatic / Q000737:chemistry; D012416:Rubredoxins / Q000737:chemistry
D003459:Crystallins; D003574:Cytochrome c Group; D005288:Ferredoxins; D005418:Flavodoxin; D007140:Immunoglobulin Fab Fragments; D010320:Parvalbumins; D010940:Plant Proteins; D012360:RNA, Transfer, Phe; D012416:Rubredoxins; D012313:RNA; C024934:crambin protein, Crambe abyssinica; D001536:Bence Jones Protein; D010970:Plastocyanin; D007611:Aprotinin; D012259:Ribonuclease, Pancreatic