-
1
-
-
0028009297
-
Knowledge-based protein modelling
-
Johnson MS, Srinivasan N, Sowdhamini R, Blundell BL: Knowledge-based protein modelling. CRC Crit Rev Biochem Mol Biol 1994, 29:1-68.
-
(1994)
CRC Crit Rev Biochem Mol Biol
, vol.29
, pp. 1-68
-
-
Johnson, M.S.1
Srinivasan, N.2
Sowdhamini, R.3
Blundell, B.L.4
-
2
-
-
0027373337
-
Knowledge-based model building of proteins: Concepts and examples
-
Bajorath J, Stenkamp R, Aruffo A: Knowledge-based model building of proteins: concepts and examples. Protein Sci 1994, 2:1798-1810.
-
(1994)
Protein Sci
, vol.2
, pp. 1798-1810
-
-
Bajorath, J.1
Stenkamp, R.2
Aruffo, A.3
-
3
-
-
0028991962
-
Modelling mutations and homologous proteins
-
Šali A: Modelling mutations and homologous proteins. Curr Opin Biotechnol 1995, 6:437-451.
-
(1995)
Curr Opin Biotechnol
, vol.6
, pp. 437-451
-
-
Šali, A.1
-
4
-
-
0029902780
-
Bridging the protein sequence-structure gap by structure predictions
-
Rost B, Sander C: Bridging the protein sequence-structure gap by structure predictions. Annu Rev Biophys Biomol Struct 1996, 25:113-136. A review of protein structure prediction methods, including secondary-structure prediction, contact prediction, comparative modelling and fold recognition.
-
(1996)
Annu Rev Biophys Biomol Struct
, vol.25
, pp. 113-136
-
-
Rost, B.1
Sander, C.2
-
5
-
-
0000187138
-
The response of protein structures to amino-acid sequence changes
-
Lesk AM, Chothia CH: The response of protein structures to amino-acid sequence changes. Phil Trans R Soc London Ser B 1986, 317:345-356.
-
(1986)
Phil Trans r Soc London Ser B
, vol.317
, pp. 345-356
-
-
Lesk, A.M.1
Chothia, Ch.2
-
6
-
-
0000338489
-
Comparison of solvent inaccessible cores of homologous proteins: Definitions useful for protein modelling
-
Hubbard TJP, Blundell TL: Comparison of solvent inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1987, 1:159-171.
-
(1987)
Protein Eng
, vol.1
, pp. 159-171
-
-
Hubbard, T.1
Blundell, T.L.2
-
7
-
-
0014693695
-
A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme
-
Browne WJ, North ACT, Phillips DC, Brew K, Vanaman TC, Hill RC: A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme. J Mol Biol 1969, 42:65-86.
-
(1969)
J Mol Biol
, vol.42
, pp. 65-86
-
-
Browne, W.J.1
North, A.C.T.2
Phillips, D.C.3
Brew, K.4
Vanaman, T.C.5
Hill, R.C.6
-
8
-
-
0019888748
-
Comparative model-building of the mammalian serine proteases
-
Greer J: Comparative model-building of the mammalian serine proteases. J Mol Biol 1981, 153:1027-1042.
-
(1981)
J Mol Biol
, vol.153
, pp. 1027-1042
-
-
Greer, J.1
-
9
-
-
0023305986
-
Knowledge-based prediction of protein structures and the design of novel molecules
-
Blundell TL, Sibanda BL, Sternberg MJE, Thornton JM: Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987, 326:347-352.
-
(1987)
Nature
, vol.326
, pp. 347-352
-
-
Blundell, T.L.1
Sibanda, B.L.2
Sternberg, M.J.E.3
Thornton, J.M.4
-
10
-
-
0022701772
-
Using known substructures in protein model building and crystallography
-
Jones TH, Thirup S: Using known substructures in protein model building and crystallography. EMBO J 1986, 5:819-822.
-
(1986)
EMBO J
, vol.5
, pp. 819-822
-
-
Jones, T.H.1
Thirup, S.2
-
11
-
-
0024395940
-
A 3-D building blocks approach to analyzing and predicting structure of proteins
-
Unger R, Harel D, Wherland W, Sussman JL: A 3-D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989, 5:355-373.
-
(1989)
Proteins
, vol.5
, pp. 355-373
-
-
Unger, R.1
Harel, D.2
Wherland, W.3
Sussman, J.L.4
-
12
-
-
0024527223
-
Modelling the polypeptide backbone with 'spare parts' from known protein structures
-
Claessens M, Cutsem EV, Lasters I, Wodak S: Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng 1989, 4:335-345.
-
(1989)
Protein Eng
, vol.4
, pp. 335-345
-
-
Claessens, M.1
Cutsem, E.V.2
Lasters, I.3
Wodak, S.4
-
13
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
Levitt M: Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992, 226:507-533.
-
(1992)
J Mol Biol
, vol.226
, pp. 507-533
-
-
Levitt, M.1
-
14
-
-
0026018780
-
A new method for building protein conformations from sequence alignments with homologues of known structure
-
Havel TF, Snow ME: A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 1991, 217:1-7.
-
(1991)
J Mol Biol
, vol.217
, pp. 1-7
-
-
Havel, T.F.1
Snow, M.E.2
-
15
-
-
0027510701
-
An automated method for modeling proteins on known templates using distance geometry
-
Srinivasan S, March CJ, Sudarsanam S: An automated method for modeling proteins on known templates using distance geometry. Protein Sci 1993, 2:227-289.
-
(1993)
Protein Sci
, vol.2
, pp. 227-289
-
-
Srinivasan, S.1
March, C.J.2
Sudarsanam, S.3
-
16
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Šali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Šali, A.1
Blundell, T.L.2
-
17
-
-
0028066936
-
Comparison of systematic search and database methods for constructing segments of protein structure
-
Fidelis K, Stern PS, Bacon D, Moult J: Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994, 7:953-960.
-
(1994)
Protein Eng
, vol.7
, pp. 953-960
-
-
Fidelis, K.1
Stern, P.S.2
Bacon, D.3
Moult, J.4
-
18
-
-
0141560472
-
Modeling side-chain conformation
-
Vásquez M: Modeling side-chain conformation. Curr Opin Struct Biol 1996, 6:217-221. The main approximations in sidechain modelling with emphasis on the rigid-backbone approximation are reviewed.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 217-221
-
-
Vásquez, M.1
-
19
-
-
0022788691
-
An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
-
Moult J, James MNG: An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1986, 1:146-163.
-
(1986)
Proteins
, vol.1
, pp. 146-163
-
-
Moult, J.1
James, M.N.G.2
-
20
-
-
0023173201
-
Prediction of the folding of short polypeptide segments by uniform conformational sampling
-
Bruccoleri RE, Karplus M: Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987, 26:137-168.
-
(1987)
Biopolymers
, vol.26
, pp. 137-168
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
21
-
-
0022842039
-
Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCP603 from many randomly generated loop conformations
-
Fine RM, Wang H, Shenkin PS, Yarmush DL, Levinthal C: Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCP603 from many randomly generated loop conformations. Proteins 1986, 1:342-362.
-
(1986)
Proteins
, vol.1
, pp. 342-362
-
-
Fine, R.M.1
Wang, H.2
Shenkin, P.S.3
Yarmush, D.L.4
Levinthal, C.5
-
23
-
-
0022531028
-
The predicted structure of immunoglobulin d1.3 and its comparison with the crystal structure
-
Chothia C, Lesk AM, Levitt M, Amit AG, Mariuzza RA, Phillips SEV, Poljak RJ: The predicted structure of immunoglobulin d1.3 and its comparison with the crystal structure. Science 1986, 233:755-758.
-
(1986)
Science
, vol.233
, pp. 755-758
-
-
Chothia, C.1
Lesk, A.M.2
Levitt, M.3
Amit, A.G.4
Mariuzza, R.A.5
Sev, P.6
Poljak, R.J.7
-
24
-
-
0029797369
-
Structural model of the anti-snake-toxin antibody, Mα2,3
-
Tenette C, Ducancel F, Smith JC: Structural model of the anti-snake-toxin antibody, Mα2,3. Proteins 1996, 26:9-31. A combination of three existing methods to model antibody CDR loops is described.
-
(1996)
Proteins
, vol.26
, pp. 9-31
-
-
Tenette, C.1
Ducancel, F.2
Smith, J.C.3
-
25
-
-
0028984808
-
Prediction of hypervariable CDR-H3 loop structures in antibodies
-
Reczko M, Martin ACR, Bohr H, Suhai S: Prediction of hypervariable CDR-H3 loop structures in antibodies. Protein Eng 1996, 8:389-395.
-
(1996)
Protein Eng
, vol.8
, pp. 389-395
-
-
Reczko, M.1
Martin, A.C.R.2
Bohr, H.3
Suhai, S.4
-
26
-
-
0029871163
-
Accuracy and reliability of the scaling-relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational samplings
-
Zheng Q, Kyle DJ: Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings. Proteins 1996, 24:209-217. An extension and evaluation of the previously published loop-modelling method is described [27].
-
(1996)
Proteins
, vol.24
, pp. 209-217
-
-
Zheng, Q.1
Kyle, D.J.2
-
27
-
-
0027164958
-
Determining protein loop conformation using scaling-relaxation techniques
-
Zheng Q, Rosenfeld RJ, Vajda S, DeLisi C: Determining protein loop conformation using scaling-relaxation techniques. Protein Sci 1993, 2:1242-1248.
-
(1993)
Protein Sci
, vol.2
, pp. 1242-1248
-
-
Zheng, Q.1
Rosenfeld, R.J.2
Vajda, S.3
DeLisi, C.4
-
28
-
-
84986512474
-
CHARMm: A program for macromolecular energy minimization and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M: CHARMm: a program for macromolecular energy minimization and dynamics calculations. J Comp Chem 1983, 4:187-217.
-
(1983)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
29
-
-
0030449155
-
Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction
-
Donate LE, Rufino SD, Canard LHJ, Blundell TL: Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996, 5:2600-2616. A classification of loops by length, sequence, mainchain conformation and relative disposition of the flanking secondary-structure segments is described.
-
(1996)
Protein Sci
, vol.5
, pp. 2600-2616
-
-
Donate, L.E.1
Rufino, S.D.2
Lhj, C.3
Blundell, T.L.4
-
30
-
-
0030596489
-
A global taxonomy of loops in globular proteins
-
Kwasigroch J-M, Chomilier J, Mornon J-P: A global taxonomy of loops in globular proteins. J Mol Biol 1996, 259:855-872. A database of loops that are clustered into families on the basis of their length and conformation is described.
-
(1996)
J Mol Biol
, vol.259
, pp. 855-872
-
-
Kwasigroch, J.-M.1
Chomilier, J.2
Mornon, J.-P.3
-
31
-
-
0028342488
-
A statistical analysis of side-chain conformations in proteins: Comparison between ECEPP predictions
-
Nayeem A, Scheraga HA: A statistical analysis of side-chain conformations in proteins: comparison between ECEPP predictions. J Protein Chem 1994, 13:283-296.
-
(1994)
J Protein Chem
, vol.13
, pp. 283-296
-
-
Nayeem, A.1
Scheraga, H.A.2
-
32
-
-
0028212927
-
Efficient rotamer elimination applied to protein side chains and related spin glasses
-
Goldstein RF: Efficient rotamer elimination applied to protein side chains and related spin glasses. Biophys J 1994, 66:1335-1340.
-
(1994)
Biophys J
, vol.66
, pp. 1335-1340
-
-
Goldstein, R.F.1
-
33
-
-
0029091449
-
Repacking proteins cores with backbone freedom: Structure prediction for coiled coils
-
Harbury PB, Tidor B, Kim PS: Repacking proteins cores with backbone freedom: structure prediction for coiled coils. Proc Natl Acad Sci USA 1995, 92:8408-8412.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 8408-8412
-
-
Harbury, P.B.1
Tidor, B.2
Kim, P.S.3
-
34
-
-
0028826985
-
Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains
-
Lasters I, De Maeyer M, Desmet J: Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains. Protein Eng 1995, 8:815-822.
-
(1995)
Protein Eng
, vol.8
, pp. 815-822
-
-
Lasters, I.1
De Maeyer, M.2
Desmet, J.3
-
35
-
-
0029015770
-
An evaluation of discrete and continuum search techniques for conformational analysis of side chains in proteins
-
Vásquez M: An evaluation of discrete and continuum search techniques for conformational analysis of side chains in proteins. Biopolymers 1995, 36:53-70.
-
(1995)
Biopolymers
, vol.36
, pp. 53-70
-
-
Vásquez, M.1
-
36
-
-
0029591934
-
Finding the global minimum: A fuzzy end elimination implementation
-
Keller DA, Shibata M, Marcus E, Ornstein RL, Rein R: Finding the global minimum: a fuzzy end elimination implementation. Protein Eng 1995, 8:893-904.
-
(1995)
Protein Eng
, vol.8
, pp. 893-904
-
-
Keller, D.A.1
Shibata, M.2
Marcus, E.3
Ornstein, R.L.4
Rein, R.5
-
37
-
-
0029058162
-
Side-chain prediction by neural networks and simulated annealing optimization
-
Hwang JK, Liao WF: Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng 1995, 8:893-904.
-
(1995)
Protein Eng
, vol.8
, pp. 893-904
-
-
Hwang, J.K.1
Liao, W.F.2
-
38
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
in press
-
Bower MJ, Cohen FE, Dunbrack RL: Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997, in press. A backbone-dependent rotamer library is tested in 'real world' comparative modelling cases using templates in the range from 30-90% sequence identity. A high prediction accuracy is obtained.
-
(1997)
J Mol Biol
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack, R.L.3
-
39
-
-
0030348040
-
Testing homology modeling on mutant proteins: Predicting structural and thermodynamic effects in the Ala98→Val mutants of T4 lysozyme
-
1 torsion rotations is shown to be less sensitive to backbone errors than the rotamer-based model.
-
(1996)
Fold des
, vol.1
, pp. 1-12
-
-
Lee, C.1
-
40
-
-
0000790849
-
From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins
-
1) probability distributions are derived for each residue type from a database of known protein structures. Their performance in main- chain/sidechain conformational searches is compared with those of some alternative probability distributions.
-
(1996)
J Comp Chem
, vol.17
, pp. 1453-1480
-
-
Cheng, B.1
Nayeem, A.2
Scheraga, H.A.3
-
41
-
-
0029811308
-
Prediction and evaluation of side-chain conformations for protein backbone structures
-
Shenkin SP, Farid H, Fetrow JS: Prediction and evaluation of side-chain conformations for protein backbone structures. Proteins 1996, 26:323-352. A rapid algorithm for sidechain rotamer prediction on a fixed backbone is described. It is based on a rotamer library and Monte Carlo search. A method for estimating prediction accuracy is proposed.
-
(1996)
Proteins
, vol.26
, pp. 323-352
-
-
Shenkin, S.P.1
Farid, H.2
Fetrow, J.S.3
-
42
-
-
0009130599
-
A structural explanation for the twilight zone of protein sequence homology
-
Chung SY, Subbiah S: A structural explanation for the twilight zone of protein sequence homology. Structure 1996, 4:1123-1127. A possible structural explanation is given for the abrupt and large changes in the sidechain-packing patterns when mainchain differences become larger than approximately 2 Å.
-
(1996)
Structure
, vol.4
, pp. 1123-1127
-
-
Chung, S.Y.1
Subbiah, S.2
-
43
-
-
0028786978
-
The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins
-
Chung SY, Subbiah S: The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins. Protein Sci 1995, 4:2300-2309.
-
(1995)
Protein Sci
, vol.4
, pp. 2300-2309
-
-
Chung, S.Y.1
Subbiah, S.2
-
45
-
-
0028223845
-
Predicting protein mutant energetics by self consistent ensemble optimisation
-
Lee C: Predicting protein mutant energetics by self consistent ensemble optimisation. J Mol Biol 1994, 236:918-939.
-
(1994)
J Mol Biol
, vol.236
, pp. 918-939
-
-
Lee, C.1
-
46
-
-
0029869187
-
Mean-field minimization methods for biological macromolecules
-
Koehl P, Delarue M: Mean-field minimization methods for biological macromolecules. Curr Opin Struct Biol 1996, 6:222-226.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 222-226
-
-
Koehl, P.1
Delarue, M.2
-
47
-
-
0023155210
-
Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder JW, Richards FM: Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987, 193:775-791.
-
(1987)
J Mol Biol
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
48
-
-
0028343413
-
Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
-
Koehl P, Delarue M: Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994, 239:249-275.
-
(1994)
J Mol Biol
, vol.239
, pp. 249-275
-
-
Koehl, P.1
Delarue, M.2
-
49
-
-
0027208112
-
Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
-
Schrauber H, Eisenhaber F, Argos P: Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 1993, 230:592-612.
-
(1993)
J Mol Biol
, vol.230
, pp. 592-612
-
-
Schrauber, H.1
Eisenhaber, F.2
Argos, P.3
-
50
-
-
0028147533
-
The crystal structure of a mutant protein with altered but improved hydrophobic core packing
-
Lim WA, Hodel A, Sauer RT, Richards FM: The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 1994, 91:423-427.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 423-427
-
-
Lim, W.A.1
Hodel, A.2
Sauer, R.T.3
Richards, F.M.4
-
51
-
-
0029565303
-
A self consistent mean field approach to simultaneous gap closure and side-chain positioning in protein homology modelling
-
Koehl P, Delarue M: A self consistent mean field approach to simultaneous gap closure and side-chain positioning in protein homology modelling. Nat Struct Biol 1995, 2:163-170.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 163-170
-
-
Koehl, P.1
Delarue, M.2
-
52
-
-
0028081403
-
Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility
-
Russell RB, Barton GJ: Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J Mol Biol 1994, 244:332-350.
-
(1994)
J Mol Biol
, vol.244
, pp. 332-350
-
-
Russell, R.B.1
Barton, G.J.2
-
53
-
-
0028232955
-
Searching protein structure databases has come of age
-
Holm L, Sander C: Searching protein structure databases has come of age. Proteins 1994, 19:165-173.
-
(1994)
Proteins
, vol.19
, pp. 165-173
-
-
Holm, L.1
Sander, C.2
-
54
-
-
0001923306
-
Protein sequence alignment and database scanning
-
Edited by Sternberg MJE. Oxford: IRL Press
-
Barton GJ: Protein sequence alignment and database scanning. In Protein Structure Prediction: A Practical Approach. Edited by Sternberg MJE. Oxford: IRL Press; 1997:31-63.
-
(1997)
Protein Structure Prediction: a Practical Approach
, pp. 31-63
-
-
Barton, G.J.1
-
55
-
-
0028864721
-
Homology modeling of an immunoglobulin-like domain in the Saccharomyces cerevisiae adhesion protein α-agglutinin
-
Lipke PN, Chen M-H, De Nobel H, Kurjan J, Kahn PC: Homology modeling of an immunoglobulin-like domain in the Saccharomyces cerevisiae adhesion protein α-agglutinin. Protein Sci 1995, 4:2168-2178. An example of a difficult comparative modelling case, which is based on a low similarity between the target and template proteins. The secondary-structure predictions are used systematically to improve the input alignment for the modelling procedure.
-
(1995)
Protein Sci
, vol.4
, pp. 2168-2178
-
-
Lipke, P.N.1
Chen, M.-H.2
De Nobel, H.3
Kurjan, J.4
Kahn, P.C.5
-
56
-
-
0029670269
-
ABGEN: A knowledge-based automated approach for antibody structure modeling
-
Mandal C, Kingery BD, Anchin JM, Subramaniam S, Linthicum DS: ABGEN: a knowledge-based automated approach for antibody structure modeling. Nat Biotechnol 1996, 14:323-328. A completely automated antibody-modelling system that uses the existing sequence and structural databases of known antibodies is described.
-
(1996)
Nat Biotechnol
, vol.14
, pp. 323-328
-
-
Mandal, C.1
Kingery, B.D.2
Anchin, J.M.3
Subramaniam, S.4
Linthicum, D.S.5
-
57
-
-
0027326222
-
Protein fold-refinement: Building models from idealized folds using motif constraints and multiple sequence data
-
Taylor WR: Protein fold-refinement: building models from idealized folds using motif constraints and multiple sequence data. Protein Eng 1993, 6:593-604.
-
(1993)
Protein Eng
, vol.6
, pp. 593-604
-
-
Taylor, W.R.1
-
58
-
-
0030322828
-
Homology modelling by distance geometry
-
Aszódi A, Taylor WR: Homology modelling by distance geometry. Fold Des 1996, 1:325-334. A description of a comparative-modelling method that is based on distance geometry is presented. The method is useful for the quick generation of a large number of low resolution models. The models consist of residues described by a Cα atom and a sidechain pseudoatom.
-
(1996)
Fold des
, vol.1
, pp. 325-334
-
-
Aszódi, A.1
Taylor, W.R.2
-
59
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel U, Sander C, Schneider R, Valencia A: Correlated mutations and residue contacts in proteins. Proteins 1994, 18:309-317.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
60
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ: Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990, 213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
61
-
-
0026538668
-
Solution structure of neuronal bungaro-toxin determined by two-dimensional NMR spectroscopy: Calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics
-
Sutcliffe MJ, Dobson CM, Oswald RE: Solution structure of neuronal bungaro-toxin determined by two-dimensional NMR spectroscopy: calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 1992, 31:2962-2970.
-
(1992)
Biochemistry
, vol.31
, pp. 2962-2970
-
-
Sutcliffe, M.J.1
Dobson, C.M.2
Oswald, R.E.3
-
62
-
-
0029010484
-
Structure of the catalytic region of human complement protease c1s: Study by chemical cross-linking and three-dimensional homology modelling
-
Rossi V, Gaboriaud C, Lacroix M, Ulrich J, Fontecilla-Camps JC, Gagnon J, Arlaud GJ: Structure of the catalytic region of human complement protease c1s: study by chemical cross-linking and three-dimensional homology modelling. Biochemistry 1995, 34:7311-7321.
-
(1995)
Biochemistry
, vol.34
, pp. 7311-7321
-
-
Rossi, V.1
Gaboriaud, C.2
Lacroix, M.3
Ulrich, J.4
Fontecilla-Camps, J.C.5
Gagnon, J.6
Arlaud, G.J.7
-
63
-
-
0029983584
-
Structure of recombinant rat UBF by electron image analysis and homology modelling
-
Neil KJ: Structure of recombinant rat UBF by electron image analysis and homology modelling. Nucleic Acids Res 1995, 24:1472-1480.
-
(1995)
Nucleic Acids Res
, vol.24
, pp. 1472-1480
-
-
Neil, K.J.1
-
64
-
-
0027297047
-
Erythropoietin structure-function relationships. Mutant proteins that test a model of tertiary structure
-
Boissel JP, Lee WR, Presnell SR, Cohen FE, Bunn HF: Erythropoietin structure-function relationships. Mutant proteins that test a model of tertiary structure. J Biol Chem 1993, 268:15983-15993.
-
(1993)
J Biol Chem
, vol.268
, pp. 15983-15993
-
-
Boissel, J.P.1
Lee, W.R.2
Presnell, S.R.3
Cohen, F.E.4
Bunn, H.F.5
-
66
-
-
0028864205
-
A critical assessment of comparative molecular modeling of tertiary structures of proteins
-
Mosimann S, Meleshko R, James MNG: A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 1995, 23:301-317.
-
(1995)
Proteins
, vol.23
, pp. 301-317
-
-
Mosimann, S.1
Meleshko, R.2
James, M.N.G.3
-
67
-
-
0028871814
-
Evaluation of comparative protein modeling by MODELLER
-
Šali A, Potterton L, Yuan F, Van Vlijmen H, Karplus M: Evaluation of comparative protein modeling by MODELLER. Proteins 1995, 23:318-326.
-
(1995)
Proteins
, vol.23
, pp. 318-326
-
-
Šali, A.1
Potterton, L.2
Yuan, F.3
Van Vlijmen, H.4
Karplus, M.5
-
68
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl MJ: Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17:355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
69
-
-
0028156696
-
Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1β
-
Ohlendorf DH: Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1β. Acta Crystallogr D 1994, 50:808-812.
-
(1994)
Acta Crystallogr D
, vol.50
, pp. 808-812
-
-
Ohlendorf, D.H.1
-
70
-
-
0027172878
-
Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy
-
Clore GM, Robien MA, Gronenborn AM: Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J Mol Biol 1993, 231:82-102.
-
(1993)
J Mol Biol
, vol.231
, pp. 82-102
-
-
Clore, G.M.1
Robien, M.A.2
Gronenborn, A.M.3
-
71
-
-
0028232369
-
An assessment of the precision and accuracy of protein structures determined by NMR
-
Zhao D, Jardetzky O: An assessment of the precision and accuracy of protein structures determined by NMR. J Mol Biol 1994, 239:601-607
-
(1994)
J Mol Biol
, vol.239
, pp. 601-607
-
-
Zhao, D.1
Jardetzky, O.2
-
72
-
-
0025047629
-
A mutant T4 lysozyme displays five different crystal conformations
-
Faber HR, Matthews BW: A mutant T4 lysozyme displays five different crystal conformations. Nature 1990, 348:263-266.
-
(1990)
Nature
, vol.348
, pp. 263-266
-
-
Faber, H.R.1
Matthews, B.W.2
-
74
-
-
0002638513
-
Protein Data Bank
-
Edited by Allen FH, Bergerhoff G, Sievers R. Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography
-
Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J: Protein Data Bank. In Crystallographic Databases Information, Content, Software Systems, Scientific Applications. Edited by Allen FH, Bergerhoff G, Sievers R. Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography; 1987:107-132.
-
(1987)
Crystallographic Databases Information, Content, Software Systems, Scientific Applications
, pp. 107-132
-
-
Abola, E.E.1
Bernstein, F.C.2
Bryant, S.H.3
Koetzle, T.F.4
Weng, J.5
-
76
-
-
0027122748
-
One thousand families for the molecular biologist
-
Chothia C: One thousand families for the molecular biologist. Nature 1992, 360:543-544.
-
(1992)
Nature
, vol.360
, pp. 543-544
-
-
Chothia, C.1
-
77
-
-
0028593509
-
Protein superfamilies and domain superfolds
-
Orengo CA, Jones DT, Thornton JM: Protein superfamilies and domain superfolds. Nature 1994, 372:631-634.
-
(1994)
Nature
, vol.372
, pp. 631-634
-
-
Orengo, C.A.1
Jones, D.T.2
Thornton, J.M.3
-
78
-
-
0029785147
-
Mapping the protein universe
-
Holm L, Sander C: Mapping the protein universe. Science 1996, 273:595-602. A review of the use of protein structure comparisons in protein classification and in function identification.
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
79
-
-
0029094503
-
Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. a cluster of histidines in mouse mast cell protease-7 regulates its binding to heparin serglycin proteoglycan
-
Matsumoto R, Šali A, Ghildyal N, Karplus M, Stevens RL: Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines in mouse mast cell protease-7 regulates its binding to heparin serglycin proteoglycan. J Biol Chem 1995, 270:19524-19531.
-
(1995)
J Biol Chem
, vol.270
, pp. 19524-19531
-
-
Matsumoto, R.1
Šali, A.2
Ghildyal, N.3
Karplus, M.4
Stevens, R.L.5
-
80
-
-
0000513014
-
Ligand specificity of brain lipid binding protein
-
Xu LZ, Sánchez R, Šali A, Heintz N: Ligand specificity of brain lipid binding protein. J Biol Chem 1996, 271:24711-24719. A comparative model of brain lipid-binding protein is used to suggest mutations for exploring ligand specificity. The mutants are expressed and validated experimentally.
-
(1996)
J Biol Chem
, vol.271
, pp. 24711-24719
-
-
Xu, L.Z.1
Sánchez, R.2
Šali, A.3
Heintz, N.4
-
81
-
-
0027480452
-
Structure-based inhibitor design by using protein models for the development of antiparasitic agents
-
Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE: Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci USA 1993, 90:3583-3587.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 3583-3587
-
-
Ring, C.S.1
Sun, E.2
McKerrow, J.H.3
Lee, G.K.4
Rosenthal, P.J.5
Kuntz, I.D.6
Cohen, F.E.7
-
82
-
-
0028095922
-
Comparison of homology models with the experimental structure of a novel serine protease
-
Carson M, Bugg CE, Delucas L, Narayana S: Comparison of homology models with the experimental structure of a novel serine protease. Acta Crystallogr D 1994, 50:889-899.
-
(1994)
Acta Crystallogr D
, vol.50
, pp. 889-899
-
-
Carson, M.1
Bugg, C.E.2
Delucas, L.3
Narayana, S.4
-
83
-
-
0029914807
-
450 2d6 based on homology modeling and NMR studies of substrate binding
-
450 2d6 based on homology modeling and NMR studies of substrate binding. Biochemistry 1996, 35:4540-4550. An example of how NMR-derived restraints can be combined with comparative modelling to improve the resulting protein model.
-
(1996)
Biochemistry
, vol.35
, pp. 4540-4550
-
-
Modi, S.1
Paine, M.J.2
Sutcliffe, M.J.3
Lian, L.-Y.4
Primrose, W.U.5
Wolf, C.R.6
Roberts, G.C.K.7
-
84
-
-
0029922311
-
Xylanase homology modelling using the inverse protein folding approach
-
Chen X, Whitmire D, Bowen JP: Xylanase homology modelling using the inverse protein folding approach. Protein Sci 1996, 5:705-708. An example of the use of threading to obtain a remotely related structure for comparative modelling.
-
(1996)
Protein Sci
, vol.5
, pp. 705-708
-
-
Chen, X.1
Whitmire, D.2
Bowen, J.P.3
-
85
-
-
0028808762
-
An approach to protein homology modelling based on an ensemble of NMR structures; application to the Sox-5 HMG-box protein
-
Adzhubei AA, Laughton CA, Neidle S: An approach to protein homology modelling based on an ensemble of NMR structures; application to the Sox-5 HMG-box protein. Protein Eng 1995, 8:615-625.
-
(1995)
Protein Eng
, vol.8
, pp. 615-625
-
-
Adzhubei, A.A.1
Laughton, C.A.2
Neidle, S.3
-
86
-
-
0029012995
-
Homology modelling of horseradish peroxidase coupled to two-dimensional NMR spectral assignments
-
Loew GH, Du P, Smith AT: Homology modelling of horseradish peroxidase coupled to two-dimensional NMR spectral assignments. Biochem Soc Trans 1995, 23:250-256.
-
(1995)
Biochem Soc Trans
, vol.23
, pp. 250-256
-
-
Loew, G.H.1
Du, P.2
Smith, A.T.3
-
87
-
-
0030601845
-
Rational molecular design and genetic engineering of herbicide resistant crops by structure modeling and site-directed mutagenesis of acetohydroxyacid synthase
-
Ott K-H, Kwagh J-G, Stockton GW, Sidorov V, Kakefuda G: Rational molecular design and genetic engineering of herbicide resistant crops by structure modeling and site-directed mutagenesis of acetohydroxyacid synthase. J Mol Biol 1996, 263:359-368. A successful application of comparative modelling to solve a real life problem.
-
(1996)
J Mol Biol
, vol.263
, pp. 359-368
-
-
Ott, K.-H.1
Kwagh, J.-G.2
Stockton, G.W.3
Sidorov, V.4
Kakefuda, G.5
-
88
-
-
0029935478
-
Comparison of an antibody model with an X-ray structure; the variable fragment of BR96
-
Bajorath J, Sheriff S: Comparison of an antibody model with an X-ray structure; the variable fragment of BR96. Proteins 1996, 24:152-157. The BR96 antibody model is compared with two X-ray structures determined after the model was built. Most of the residues important for interaction with an antigen were identified correctly.
-
(1996)
Proteins
, vol.24
, pp. 152-157
-
-
Bajorath, J.1
Sheriff, S.2
-
89
-
-
0030342727
-
Helmholtz free energies of atom pair interactions in proteins
-
Sippl MJ, Ortner M, Jaritz M, Lackner P, Flöckner H: Helmholtz free energies of atom pair interactions in proteins. Fold Des 1996, 1:275-288. Statistical potentials for atom-atom distances are described. Potentials like this one will probably be useful in improving the accuracy of comparative modelling.
-
(1996)
Fold des
, vol.1
, pp. 275-288
-
-
Sippl, M.J.1
Ortner, M.2
Jaritz, M.3
Lackner, P.4
Flöckner, H.5
-
90
-
-
0029844461
-
Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
-
DeBot SE, Skolnick J: Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. Protein Eng 1996, 9:937-955. Statistical potentials that could in principle be used to improve the accuracy of comparative models are described.
-
(1996)
Protein Eng
, vol.9
, pp. 937-955
-
-
DeBot, S.E.1
Skolnick, J.2
-
91
-
-
0028326042
-
Monte Carlo simulations of protein folding. II Application to protein A, ROP, and crambin
-
Kolinski A, Skolnick J: Monte Carlo simulations of protein folding. II Application to protein A, ROP, and crambin. Proteins 1994, 18:353-366.
-
(1994)
Proteins
, vol.18
, pp. 353-366
-
-
Kolinski, A.1
Skolnick, J.2
-
92
-
-
0027361123
-
A structural basis for sequence comparisons: An evaluation of scoring methodologies
-
Johnson MS, Overington JP: A structural basis for sequence comparisons: an evaluation of scoring methodologies. J Mol Biol 1993, 233:716-738.
-
(1993)
J Mol Biol
, vol.233
, pp. 716-738
-
-
Johnson, M.S.1
Overington, J.P.2
-
94
-
-
0029982530
-
The structural alignment between two proteins: Is there a unique answer?
-
•] show that a unique structure-structure alignment is not always guaranteed when the compared structures are sufficiently different.
-
(1996)
Protein Sci
, vol.5
, pp. 1325-1338
-
-
Godzik, A.1
-
95
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Lütthy R, Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lütthy, R.2
Eisenberg, D.3
-
96
-
-
0026418178
-
A search for the most stable folds of protein chains
-
Finkelstein AV, Reva BA: A search for the most stable folds of protein chains. Nature 1991, 351:497-499.
-
(1991)
Nature
, vol.351
, pp. 497-499
-
-
Finkelstein, A.V.1
Reva, B.A.2
-
97
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM: A new approach to protein fold recognition. Nature 1992, 358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
98
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A, Kolinski A, Skolnick J: Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 1992, 227:227-238.
-
(1992)
J Mol Biol
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
99
-
-
0343961969
-
Structural diversity in a family of homologous proteins
-
Pawlowski K, Bierzynski A, Godzik A: Structural diversity in a family of homologous proteins. J Mol Biol 1996, 258:349-366. Comparative models for the EF-hand calcium-binding proteins are calculated from a number of different templates. The models are compared with the actual structures and evaluated with respect to several energetic criteria. Putative energy factors responsible for the selection of the particular quaternary structure among several alternatives are identified.
-
(1996)
J Mol Biol
, vol.258
, pp. 349-366
-
-
Pawlowski, K.1
Bierzynski, A.2
Godzik, A.3
-
100
-
-
0001433241
-
Knowledge based modelling of homologous proteins. Part I: Three dimensional frameworks derived from the simultaneous superposition of multiple structures
-
Sutcliffe MJ, Haneef I, Carney C, Blundell TL: Knowledge based modelling of homologous proteins. Part I: three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1987, 1:377-384.
-
(1987)
Protein Eng
, vol.1
, pp. 377-384
-
-
Sutcliffe, M.J.1
Haneef, I.2
Carney, C.3
Blundell, T.L.4
-
101
-
-
0027794968
-
Application of systematic conformational search to protein modeling
-
Bruccoleri RE: Application of systematic conformational search to protein modeling. Molecular Simulation 1993, 10:151-174.
-
(1993)
Molecular Simulation
, vol.10
, pp. 151-174
-
-
Bruccoleri, R.E.1
-
102
-
-
0027466730
-
Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipolyated H-protein from the pea leaf glycine cleavage system: A new automated methods for the prediction of protein tertiary structure
-
Brocklehurst SM, Perham RN: Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipolyated H-protein from the pea leaf glycine cleavage system: a new automated methods for the prediction of protein tertiary structure. Protein Sci 1993, 2:626-639.
-
(1993)
Protein Sci
, vol.2
, pp. 626-639
-
-
Brocklehurst, S.M.1
Perham, R.N.2
-
103
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend G: WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990, 8:52-56.
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
104
-
-
0027473885
-
A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors
-
Peitsch MC, Jongeneel CV: A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors. Int Immunol 1993, 5:233-238.
-
(1993)
Int Immunol
, vol.5
, pp. 233-238
-
-
Peitsch, M.C.1
Jongeneel, C.V.2
-
105
-
-
0027800451
-
Predicting the structure of the flavodoxin from Escherichia coli by homology modeling, distance geometry and molecular dynamics
-
Havel TF: Predicting the structure of the flavodoxin from Escherichia coli by homology modeling, distance geometry and molecular dynamics. Mol Simulation 1993, 10:175-210.
-
(1993)
Mol Simulation
, vol.10
, pp. 175-210
-
-
Havel, T.F.1
|