-
1
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
Bower, M.J., Cohen, F.E., and Dunbrack Jr., R.L. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J. Mol. Biol. 267: 1268-1282.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1268-1282
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack R.L., Jr.3
-
3
-
-
0029920337
-
Protein design automation
-
Dahiyat, B.I. and Mayo, S.L. 1996. Protein design automation. Protein Sci. 5: 895-903.
-
(1996)
Protein Sci.
, vol.5
, pp. 895-903
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
4
-
-
0030623575
-
All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side-chains by dead-end elimination
-
De Maeyer, M., Desmet, J., and Lasters, I. 1997. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side-chains by dead-end elimination. Fold Des. 2: 53-66.
-
(1997)
Fold Des.
, vol.2
, pp. 53-66
-
-
De Maeyer, M.1
Desmet, J.2
Lasters, I.3
-
5
-
-
0034575680
-
The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance
-
-. 2000. The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance. Methods Mol. Biol. 143: 265-304.
-
(2000)
Methods Mol. Biol.
, vol.143
, pp. 265-304
-
-
-
6
-
-
0028858499
-
De novo design of the hydrophobic cores of proteins
-
Desjarlais, J.R. and Handel, T.M. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci. 4: 2006-2018.
-
(1995)
Protein Sci.
, vol.4
, pp. 2006-2018
-
-
Desjarlais, J.R.1
Handel, T.M.2
-
7
-
-
0026589733
-
The dead-end elimination theorem and its use in protein side-chain positioning
-
Desmet, J., De Maeyer, M., Hazes, B., and Lasters, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356: 539-542.
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
De Maeyer, M.2
Hazes, B.3
Lasters, I.4
-
8
-
-
0031306143
-
Theoretical and algorithmical optimization of the dead-end elimination theorem
-
Desmet, J., De Maeyer, M., and Lasters, I. 1997. Theoretical and algorithmical optimization of the dead-end elimination theorem. Pac. Symp. Biocomput. 1997: 122-133.
-
(1997)
Pac. Symp. Biocomput.
, vol.1997
, pp. 122-133
-
-
Desmet, J.1
De Maeyer, M.2
Lasters, I.3
-
9
-
-
0036643430
-
Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization
-
Desmet, J., Spriet, J., and Lasters, I. 2002. Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. Proteins 48: 31-43.
-
(2002)
Proteins
, vol.48
, pp. 31-43
-
-
Desmet, J.1
Spriet, J.2
Lasters, I.3
-
10
-
-
0032613301
-
Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
-
Dunbrack Jr., R.L. 1999. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Proteins 3: 81-87.
-
(1999)
Proteins
, vol.3
, pp. 81-87
-
-
Dunbrack R.L., Jr.1
-
11
-
-
0036667731
-
Rotamer libraries in the 21st century
-
-. 2002. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12: 431-440.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 431-440
-
-
-
12
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack Jr., R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
-
(1997)
Protein Sci.
, vol.6
, pp. 1661-1681
-
-
Dunbrack R.L., Jr.1
Cohen, F.E.2
-
13
-
-
0027160197
-
Backbone-dependent rotamer library for proteins: Application to side-chain prediction
-
Dunbrack Jr., R.L. and Karplus, M. 1993. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J. Mol. Biol. 230: 543-574.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 543-574
-
-
Dunbrack R.L., Jr.1
Karplus, M.2
-
14
-
-
0028429178
-
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
-
-. 1994, Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature Struct. Biol. 1: 334-340.
-
(1994)
Nature Struct. Biol.
, vol.1
, pp. 334-340
-
-
-
15
-
-
0028212927
-
Efficient rotamer elimination applied to protein side-chains and related spin glasses
-
Goldstein, R.F. 1994. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 66: 1335-1340.
-
(1994)
Biophys. J.
, vol.66
, pp. 1335-1340
-
-
Goldstein, R.F.1
-
16
-
-
0033200183
-
Branch-and-terminate: A combinatorial optimization algorithm for protein design
-
Gordon, D.B. and Mayo, S.L. 1999. Branch-and-terminate: A combinatorial optimization algorithm for protein design. Structure Fold Des. 7: 1089-1098.
-
(1999)
Structure Fold Des.
, vol.7
, pp. 1089-1098
-
-
Gordon, D.B.1
Mayo, S.L.2
-
17
-
-
0025978283
-
Database algorithm for generating protein back-bone and sidechain coordinates from a Ca trace: Application to model building and detection of coordinate errors
-
Holm, L. and Sander, C. 1991. Database algorithm for generating protein back-bone and sidechain coordinates from a Ca trace: Application to model building and detection of coordinate errors. J. Mol. Biol. 218: 183-194.
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 183-194
-
-
Holm, L.1
Sander, C.2
-
18
-
-
0029058162
-
Side-chain prediction by neural networks and simulated annealing optimization
-
Hwang, J.K. and Liao, W.F. 1995. Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng. 8: 363-370.
-
(1995)
Protein Eng.
, vol.8
, pp. 363-370
-
-
Hwang, J.K.1
Liao, W.F.2
-
19
-
-
0029591934
-
Finding the global minimum: A fuzzy end elimination implementation
-
Keller, D.A., Shibata, M., Marcus, E., Ornstein, R.L., and Rein, R. 1995. Finding the global minimum: A fuzzy end elimination implementation. Protein Eng. 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
-
20
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley, L.A., MacCallum, R.M., and Stemberg, M.J. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Stemberg, M.J.3
-
21
-
-
0029565303
-
A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling
-
Koehl, P. and Delarue, M. 1995. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nat. Struct. Biol. 2: 163-170.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 163-170
-
-
Koehl, P.1
Delarue, M.2
-
22
-
-
0028304155
-
Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry
-
Kono, H. and Doi, J. 1994. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry. Proteins 19: 244-255.
-
(1994)
Proteins
, vol.19
, pp. 244-255
-
-
Kono, H.1
Doi, J.2
-
23
-
-
0003460091
-
-
CRC Press, Boca Raton, FL
-
Kreher, D.L. and Stinson, D.R. 1999. Combinatorial algorithms: Generation, enumeration, and search. CRC Press, Boca Raton, FL.
-
(1999)
Combinatorial Algorithms: Generation, Enumeration, and Search
-
-
Kreher, D.L.1
Stinson, D.R.2
-
24
-
-
0027493639
-
The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem
-
Lasters, I. and Desmet, J. 1993. The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng. 6: 717-722.
-
(1993)
Protein Eng.
, vol.6
, pp. 717-722
-
-
Lasters, I.1
Desmet, J.2
-
25
-
-
0028826985
-
Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains
-
Lasters, I., DeMaeyer, M., and Desmet, J. 1995. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains. Protein Eng. 8: 815-822.
-
(1995)
Protein Eng.
, vol.8
, pp. 815-822
-
-
Lasters, I.1
DeMaeyer, M.2
Desmet, J.3
-
26
-
-
0028140474
-
Prediction of protein side-chain conformations from local three-dimensional homology relationships
-
Laughton, C.A. 1994. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J. Mol. Biol. 235: 1088-1097.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1088-1097
-
-
Laughton, C.A.1
-
27
-
-
0026019108
-
Prediction of protein side-chain conformation by packing optimization
-
Lee, C. and Subbiah, S. 1991. Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 217: 373-388.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 373-388
-
-
Lee, C.1
Subbiah, S.2
-
28
-
-
0036149564
-
Side-chain modeling with an optimized scoring function
-
Liang, S. and Grishin, N.V. 2002. Side-chain modeling with an optimized scoring function. Protein Sci. 11: 322-331.
-
(2002)
Protein Sci.
, vol.11
, pp. 322-331
-
-
Liang, S.1
Grishin, N.V.2
-
29
-
-
0035896029
-
Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
-
Looger, L.L. and Hellinga, H.W. 2001. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics. J. Mol. Biol. 307: 429-445.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 429-445
-
-
Looger, L.L.1
Hellinga, H.W.2
-
30
-
-
0034663722
-
The penultimate rotamer library
-
Lovell, S.C., Word, J.M., Richardson, J.S., and Richardson, D.C. 2000. The penultimate rotamer library. Proteins 40: 389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
31
-
-
0023521842
-
Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
-
McGregor, M.J., Islam, S.A., and Sternberg, M.J.E. 1987. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198: 295-310.
-
(1987)
J. Mol. Biol.
, vol.198
, pp. 295-310
-
-
McGregor, M.J.1
Islam, S.A.2
Sternberg, M.J.E.3
-
32
-
-
0032732306
-
Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model
-
Mendes, J., Baptista, A.M., Carrondo, M.A., and Soares, C.M. 1999a. Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model. Proteins 37: 530-543.
-
(1999)
Proteins
, vol.37
, pp. 530-543
-
-
Mendes, J.1
Baptista, A.M.2
Carrondo, M.A.3
Soares, C.M.4
-
33
-
-
0033042104
-
Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction
-
Mendes, J., Soares, C.M., and Carrondo, M.A. 1999b. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers 50: 111-131.
-
(1999)
Biopolymers
, vol.50
, pp. 111-131
-
-
Mendes, J.1
Soares, C.M.2
Carrondo, M.A.3
-
34
-
-
0034748018
-
Implicit solvation in the self-consistent mean field theory method: Side-chain modeling and prediction of folding free energies of protein mutants
-
Mendes, J., Baptista, A.M., Carrondo, M.A., and Soares, C.M. 2001a. Implicit solvation in the self-consistent mean field theory method: Side-chain modeling and prediction of folding free energies of protein mutants. J. Comp. Aided. Mol. Design 15: 721-740.
-
(2001)
J. Comp. Aided. Mol. Design
, vol.15
, pp. 721-740
-
-
Mendes, J.1
Baptista, A.M.2
Carrondo, M.A.3
Soares, C.M.4
-
35
-
-
0034957437
-
Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure
-
Mendes, J., Nagarajaram, H.A., Soares, C.M., Blundell, T.L., and Carrondo, M.A. 2001b. Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure. Biopolymers 59: 72-86.
-
(2001)
Biopolymers
, vol.59
, pp. 72-86
-
-
Mendes, J.1
Nagarajaram, H.A.2
Soares, C.M.3
Blundell, T.L.4
Carrondo, M.A.5
-
36
-
-
0001114311
-
Conformational splitting: A more powerful criterion for dead-end elimination
-
Pierce, N.A., Spriet, J.A., Desmet, J., and Mayo, S.L, 1999. Conformational splitting: A more powerful criterion for dead-end elimination. J. Comp. Chem. 21: 999-1009.
-
(1999)
J. Comp. Chem.
, vol.21
, pp. 999-1009
-
-
Pierce, N.A.1
Spriet, J.A.2
Desmet, J.3
Mayo, S.L.4
-
37
-
-
0023155210
-
Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder, J.W. and Richards, F.M. 1987. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193: 775-792.
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 775-792
-
-
Ponder, J.W.1
Richards, F.M.2
-
38
-
-
0031794714
-
Determinants of side chain conformational preferences in protein structures
-
Samudrala, R. and Moult, J. 1998. Determinants of side chain conformational preferences in protein structures, Protein Eng. 11: 991-997.
-
(1998)
Protein Eng.
, vol.11
, pp. 991-997
-
-
Samudrala, R.1
Moult, J.2
-
39
-
-
0024816521
-
Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin
-
Summers, N.L. and Karplus, M. 1989. Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin. J. Mol. Biol. 210: 785-811.
-
(1989)
J. Mol. Biol.
, vol.210
, pp. 785-811
-
-
Summers, N.L.1
Karplus, M.2
-
40
-
-
0001790593
-
Depth first search and linear graph algorithms
-
Tarjan, R. 1972. Depth first search and linear graph algorithms. SIAM J. Comput. 1: 146-160.
-
(1972)
SIAM J. Comput.
, vol.1
, pp. 146-160
-
-
Tarjan, R.1
-
41
-
-
0026179489
-
A new approach to the rapid determination of protein side chain conformations
-
Tuffery, P., Etchebest, C. Hazout, S., and Lavery, R. 1991. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8: 1267-1289.
-
(1991)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 1267-1289
-
-
Tuffery, P.1
Etchebest, C.2
Hazout, S.3
Lavery, R.4
-
42
-
-
0034625322
-
Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
-
Voigt, C.A., Gordon, D.B., and Mayo, S.L. 2000. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol. 299: 789-803.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 789-803
-
-
Voigt, C.A.1
Gordon, D.B.2
Mayo, S.L.3
-
43
-
-
0043180474
-
PISCES: A protein sequence culling server
-
in press
-
Wang, G. and Dunbrack Jr., R.L. 2003. PISCES: A protein sequence culling server. Bioinformatics (in press).
-
(2003)
Bioinformatics
-
-
Wang, G.1
Dunbrack R.L., Jr.2
-
44
-
-
0027480460
-
Modeling side-chain conformation for homologous proteins using an energy-based rotamer search
-
Wilson, C., Gregoret, L., and Agard, D. 1993. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol. 229: 996-1006.
-
(1993)
J. Mol. Biol.
, vol.229
, pp. 996-1006
-
-
Wilson, C.1
Gregoret, L.2
Agard, D.3
-
45
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
-
Word, J.M., Lovell, S.C., LaBean, T.H., Taylor, H.C., Zalis, M.E., Presley, B.K., Richardson, J.S., and Richardson, D.C. 1999a. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 285: 1711-1733.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
LaBean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
Presley, B.K.6
Richardson, J.S.7
Richardson, D.C.8
-
46
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word, J.M., Lovell, S.C., Richardson, J.S., and Richardson, D.C. 1999b. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285: 1735-1747.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
47
-
-
0035838974
-
Extending the accuracy limits of prediction for side-chain conformations
-
Xiang, Z. and Honig, B. 2001. Extending the accuracy limits of prediction for side-chain conformations. J. Mol. Biol. 311: 421-430.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 421-430
-
-
Xiang, Z.1
Honig, B.2
|