A method for predicting protein structure from sequence

Bowie, 1991, A method to identify protein sequences that fold into a known three-dimensional structure, Science, 253, 164, 10.1126/science.1853201 Sippl, 1992, Detection of native-like models for amino-acid sequences of unknown three-dimensional structure in a database of known protein conformations, Proteins, 13, 258, 10.1002/prot.340130308 Maiorov, 1992, Contact potential that recognizes the correct folding of globular proteins, J Mot Biol, 227, 876, 10.1016/0022-2836(92)90228-C Godzik, 1992, A topology fingerprint approach to the inverse folding problem, J Mot Biol, 227, 227, 10.1016/0022-2836(92)90693-E Jones, 1992, A new approach to protein fold recognition, Nature, 358, 86, 10.1038/358086a0 Ripoll, 1991, On the multiple minima problem in the conformational analysis of polypeptides, Proteins, 10, 188, 10.1002/prot.340100304 Skolnick, 1989, Computer simulations of globular protein folding and tertiary structure, Annu Rev Phys Chem, 40, 207, 10.1146/annurev.pc.40.100189.001231 Levitt, 1975, Computer simulation of protein folding, Nature, 253, 69498, 10.1038/253694a0 Kuntz, 1976, Calculation of protein tertiary structure, J Mol Biol, 106, 983, 10.1016/0022-2836(76)90347-8 Hagler, 1978, On the formation of protein tertiary structure on a computer, 75, 554 Wilson, 1989, A computer model to dynamically simulate protein folding: studies with crambin, Proteins, 6, 193, 10.1002/prot.340060208 Ycas, 1990, Computing tertiary structures of proteins, J Prot Chem, 9, 177, 10.1007/BF01025309 Dolgikh, 1981, α-lactalbumin: compact state with fluctuating tertiary structure?, FEBS Lett, 136, 311, 10.1016/0014-5793(81)80642-4 Kuwajima, 1989, The molten globule, Proteins, 6, 87, 10.1002/prot.340060202 Kolinski, 1993, A general method for the prediction of the three-dimensional structure and folding pathway of globular proteins. Application to designed helical proteins, J Chem Phys, 98, 7420, 10.1063/1.464706 Kolinski, 1992, Discretized model of proteins. I: Monte Carlo study of cooperativity in homopolypeptides, J Phys Chem, 97, 9412, 10.1063/1.463317 Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211 Skolnick J: Lattice parameter set. Available via anonymous ftp from scripps.ftp. Uhlen, 1984, Complete sequence of the Staphylococcal gene encoding protein, J Biol Chem, 259, 1695, 10.1016/S0021-9258(17)43463-6 Deisenhofer, 1981, Crystallographic refinement and atomic models of a human FC fragment and its complex with fragment B of protein A from Staphylococcus areus at 2.9 Å resolution, Biochemistry, 20, 2361, 10.1021/bi00512a001 Gouda, 1992, Three-dimensional solution structure of the B-domain of Staphylococcal Protein A: comparisons of the solution and crystal structures, Biochemistry, 40, 9665, 10.1021/bi00155a020 1986, 1 Banner, 1987, Structure of the ColEl rop protein at 1.7 Å resolution, J Mol Biol, 196, 657, 10.1016/0022-2836(87)90039-8 Godzik A, Kolinski A, Skolnick J: Lattice representation of globular proteins: how good they are and how good are they?J Comp Chem, in press. Brooks, 1983, CHARMM: a program for macromolecutar energy, minimization and dynamics calculations, J Comp Chem, 4, 187, 10.1002/jcc.540040211 Pearlman, 1991 Raleigh, 1992, A de novo designed protein shows a thermally induced transition from a native to a molten globule-like state, J Am Chem Soc, 114, 10079, 10.1021/ja00051a061 Godzik, 1993, De novo and inverse folding predictions of protein structure and dynamics, J Comp Aided Mol Des, 10.1007/BF02337559 Handel, 1992, A designed 4-helical bundle shows characteristics of both molten globule and native state, Biophysical J, 61, A265 Rey, 1992, Analytical reconstruction of a protein backbone from the α-carbon coordinates, J Comp Chem, 13, 443, 10.1002/jcc.540130407 Bernstein, 1977, The protein data bank: a computerbased archival file for macromolecular structures, J Mol Biol, 112, 535, 10.1016/S0022-2836(77)80200-3 Nikishawa, 1986, Radial locations of amino-acid residues in a globular protein: correlation with the sequence, J Biochemistry, 100, 1043, 10.1093/oxfordjournals.jbchem.a121783 Hill, 1956 Murzin, 1988, General architecture of the ahelical globule, J Mol Biol, 204, 749, 10.1016/0022-2836(88)90366-X Brunger, 1986, Three dimensional structure of proteins determined by molecular dynamics with interproton distance restraints, 83, 3801