Homology modelling by distance geometry
Tài liệu tham khảo
Browne, 1969, A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hens egg-white lysozyme, J. Mol. Biol, 42, 65, 10.1016/0022-2836(69)90487-2
Šali, 1995, Modeling mutations and homologous proteins, Curr. Opin. Biotechnol, 6, 437, 10.1016/0958-1669(95)80074-3
Crippen, 1988
Kuntz, 1989, Distance geometry, Methods Enzymol, 177, 159, 10.1016/0076-6879(89)77011-7
Havel, 1991, An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance, Prog. Biophys. Mol. Biol, 56, 43, 10.1016/0079-6107(91)90007-F
James, 1994, Computational strategies pertinent to NMR solution structure determination, Curr. Opin. Struct. Biol, 4, 275, 10.1016/S0959-440X(94)90320-4
Havel, 1991, A new method for building protein conformations from sequence alignments with homologues of known structure, J. Mol. Biol, 217, 1, 10.1016/0022-2836(91)90603-4
Havel, 1993, Predicting the structure of the flavodoxin from Escherichia coli by homology modelling, distance geometry and molecular dynamics, Molecular Simulations, 10, 175, 10.1080/08927029308022164
Srinivasan, 1993, An automated method for modeling proteins on known templates using distance geometry, Protein Sci, 2, 277, 10.1002/pro.5560020216
Sudarsanam, 1994, Homology modeling of divergent proteins, J. Mol. Biol, 241, 143, 10.1006/jmbi.1994.1484
Aszódi, 1994, Secondary structure formation in model polypeptide chains, Protein Eng, 7, 633, 10.1093/protein/7.5.633
Aszódi, 1995, Global fold determination from a small number of distance restraints, J. Mol. Biol, 251, 308, 10.1006/jmbi.1995.0436
Aszódi, 1996, Hierarchic inertial projection: a fast distance matrix embedding algorithm, Computers & Chemistry
McLachlan, 1979, Gene duplications in the structural evolution of chymotrypsin, J. Mol. Biol, 128, 49, 10.1016/0022-2836(79)90308-5
Gutin, 1994, Statistical mechanics of polymers with distance constraints, J. Chem. Phys, 100, 5290, 10.1063/1.467193
Kuszewski, 1992, Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm, J. Biomol. NMR, 2, 33, 10.1007/BF02192799
Taylor, 1988, A flexible method to align large numbers of biological sequences, J. Mol. Evol, 28, 161, 10.1007/BF02143508
Taylor, 1989, Protein structure alignment, J. Mol. Biol, 208, 1, 10.1016/0022-2836(89)90084-3
Taylor, 1994, Multiple protein structure alignment, Protein Sci, 3, 1858, 10.1002/pro.5560031025
Risler, 1988, Amino acid substitutions in structurally related proteins – a pattern-recognition approach – determination of a new and efficient scoring matrix, J. Mol. Biol, 204, 1019, 10.1016/0022-2836(88)90058-7
Dayhoff, 1978, A model of evolutionary change in proteins, 345
Aszódi, 1995, Estimating polypeptide alpha-carbon distances from multiple sequence alignments, J. Math. Chem, 17, 167, 10.1007/BF01164846
Kabsch, 1983, Dictionary of protein structure: pattern recognition by hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211
Flory, 1969
Acharya, 1989, Refined structure of baboon alphalactalbumin at 1.7 angstroms resolution. Comparison with C-type lysozyme, J. Mol. Biol, 208, 99, 10.1016/0022-2836(89)90091-0
Wilson, 1992, Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme, J. Biol. Chem, 267, 10842, 10.1016/S0021-9258(19)50095-3
Watenpaugh, 1973, The binding of riboflavin-5-phosphate in a flavoprotein. Flavodoxin at 2.0 angstroms resolution, Proc. Natl. Acad. Sci. USA, 70, 3857, 10.1073/pnas.70.12.3857
Fukuyama, 1992, Crystal structure of oxidized flavodoxin from a red alga Chondrus crispus refined at 1.8 angstrom resolution. Description of the flavin mononucleotide binding site, J. Mol. Biol, 225, 775, 10.1016/0022-2836(92)90400-E
Smith, 1977, Structure of the semiquinone form of flavodoxin from Clostridium mp. Extension of 1.8 angstroms resolution and some comparisons with the oxidized state, J. Mol. Biol, 117, 195, 10.1016/0022-2836(77)90031-6