@article {291, title = {TOUCHSTONEX: protein structure prediction with sparse NMR data}, journal = {Proteins}, volume = {53}, year = {2003}, month = {2003 Nov 1}, pages = {290-306}, abstract = {TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly represents C(alpha), C(beta), and the sidechain centers of mass. The force field consists of knowledge-based terms to produce protein-like behavior, including various short-range interactions, hydrogen bonding, and one-body, pairwise, and multibody long-range interactions. Contact restraints were incorporated into the force field as an NOE-specific pairwise potential. We evaluated the algorithm using a set of 125 proteins of various secondary structure types and lengths up to 174 residues. Using N/8 simulated, long-range sidechain contact restraints, where N is the number of residues, 108 proteins were folded to a C(alpha)-root-mean-square deviation (RMSD) from native below 6.5 A. The average RMSD of the lowest RMSD structures for all 125 proteins (folded and unfolded) was 4.4 A. The algorithm was also applied to limited experimental NOE data generated for three proteins. Using very few experimental sidechain contact restraints, and a small number of sidechain-main chain and main chain-main chain contact restraints, we folded all three proteins to low-to-medium resolution structures. The algorithm can be applied to the NMR structure determination process or other experimental methods that can provide tertiary restraint information, especially in the early stage of structure determination, when only limited data are available.}, keywords = {Algorithms, Amino Acids, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Proteins, Staphylococcal Protein A}, issn = {1097-0134}, doi = {10.1002/prot.10499}, author = {Wei Li and Yang Zhang and Daisuke Kihara and Yuanpeng Janet Huang and Deyou Zheng and Gaetano T. Montelione and Andrzej Koli{\'n}ski and Jeffrey Skolnick} } @article {287, title = {Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme}, journal = {Proteins}, volume = {18}, year = {1994}, month = {1994 Apr}, pages = {338-52}, abstract = {A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three-dimensional structure is proposed. The reduced representation of the protein alpha-carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents C alpha traces of native proteins with an accuracy of 1.0 (0.7) A rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994), the method is applied to three small globular proteins.}, keywords = {Amino Acid Sequence, Amino Acids, Computer Simulation, Hydrogen Bonding, Models, Chemical, Models, Molecular, Models, Theoretical, Molecular Sequence Data, Monte Carlo Method, Protein Folding, Protein Structure, Tertiary}, issn = {0887-3585}, doi = {10.1002/prot.340180405}, author = {Andrzej Koli{\'n}ski and Jeffrey Skolnick} }