TY - JOUR T1 - MONSSTER: a method for folding globular proteins with a small number of distance restraints JF - Journal of Molecular Biology Y1 - 1997 A1 - Jeffrey Skolnick A1 - Andrzej KoliƄski A1 - Angel. R. Ortiz KW - Algorithms KW - Aprotinin KW - Aprotinin: chemistry KW - Bacterial Proteins KW - Bacterial Proteins: chemistry KW - Computer Graphics KW - Computer Simulation KW - Flavodoxin KW - Flavodoxin: chemistry KW - Models KW - Molecular KW - Myoglobin KW - Myoglobin: chemistry KW - Plastocyanin KW - Plastocyanin: chemistry KW - Protein Conformation KW - Protein Folding KW - Protein Structure KW - Secondary KW - Tertiary KW - Thioredoxins KW - Thioredoxins: chemistry AB - The MONSSTER (MOdeling of New Structures from Secondary and TEritary Restraints) method for folding of proteins using a small number of long-distance restraints (which can be up to seven times less than the total number of residues) and some knowledge of the secondary structure of regular fragments is described. The method employs a high-coordination lattice representation of the protein chain that incorporates a variety of potentials designed to produce protein-like behaviour. These include statistical preferences for secondary structure, side-chain burial interactions, and a hydrogen-bond potential. Using this algorithm, several globular proteins (1ctf, 2gbl, 2trx, 3fxn, 1mba, 1pcy and 6pti) have been folded to moderate-resolution, native-like compact states. For example, the 68 residue 1ctf molecule having ten loosely defined, long-range restraints was reproducibly obtained with a C alpha-backbone root-mean-square deviation (RMSD) from native of about 4. A. Flavodoxin with 35 restraints has been folded to structures whose average RMSD is 4.28 A. Furthermore, using just 20 restraints, myoglobin, which is a 146 residue helical protein, has been folded to structures whose average RMSD from native is 5.65 A. Plastocyanin with 25 long-range restraints adopts conformations whose average RMSD is 5.44 A. Possible applications of the proposed approach to the refinement of structures from NMR data, homology model-building and the determination of tertiary structure when the secondary structure and a small number of restraints are predicted are briefly discussed. VL - 265 UR - http://www.ncbi.nlm.nih.gov/pubmed/9020984 ER -