-
1
-
-
14544303007
-
NP-hardness results for protein side-chain packing
-
Universal Academy Press, Tokyo
-
Akutsu T. NP-hardness results for protein side-chain packing. Genome Informatics 1997, vol. 8:180-186. Universal Academy Press, Tokyo.
-
(1997)
Genome Informatics
, vol.8
, pp. 180-186
-
-
Akutsu, T.1
-
2
-
-
0030945495
-
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
-
Alexov E.G., Gunner M.R. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys. J. 1997, 72:2075-2093.
-
(1997)
Biophys. J.
, vol.72
, pp. 2075-2093
-
-
Alexov, E.G.1
Gunner, M.R.2
-
3
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins nucleic-acids, and organic-molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A 2nd generation force-field for the simulation of proteins nucleic-acids, and organic-molecules. J. Am. Chem. Soc. 1995, 117:5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
4
-
-
0030793767
-
De novo protein design: fully automated sequence selection
-
Dahiyat B.I., Mayo S.L. De novo protein design: fully automated sequence selection. Science 1997, 278:82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
5
-
-
0026589733
-
The dead-end elimination theorem and its use in protein side-chain positioning
-
Desmet J., De Maeyer M., Hazes B., Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992, 346:539-542.
-
(1992)
Nature
, vol.346
, pp. 539-542
-
-
Desmet, J.1
De Maeyer, M.2
Hazes, B.3
Lasters, I.4
-
6
-
-
0027692037
-
Complexity of protein-folding
-
Fraenkel A.S. Complexity of protein-folding. Bull. Math. Biol. 1993, 55:1199-1210.
-
(1993)
Bull. Math. Biol.
, vol.55
, pp. 1199-1210
-
-
Fraenkel, A.S.1
-
7
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
-
Georgescu R.E., Alexov E.G., Gunner M.R. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys. J. 2002, 83:1731-1748.
-
(2002)
Biophys. J.
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
8
-
-
0028212927
-
Efficient rotamer elimination applied to protein side-chains and related spin-glasses
-
Goldstein R.F. 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
-
9
-
-
0037472680
-
Exact rotamer optimization for protein design
-
Gordon D.B., Hom G.K., Mayo S.L., Pierce N.A. Exact rotamer optimization for protein design. J. Comput. Chem. 2003, 24:232-243.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 232-243
-
-
Gordon, D.B.1
Hom, G.K.2
Mayo, S.L.3
Pierce, N.A.4
-
10
-
-
0028237287
-
Optimal sequence selection in proteins of known structure by simulated evolution
-
Hellinga H.W., Richards F.M. Optimal sequence selection in proteins of known structure by simulated evolution. Proc. Natl. Acad. Sci. U.S.A. 1994, 91:5803-5807.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 5803-5807
-
-
Hellinga, H.W.1
Richards, F.M.2
-
11
-
-
0033537993
-
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
-
Jones D.T. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 1999, 287:797-815.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
12
-
-
0001536737
-
Conformational searching methods for small molecules. 2. Genetic algorithm approach
-
Judson R.S., Jaeger E.P., Treasurywala A.M., Peterson M.L. Conformational searching methods for small molecules. 2. Genetic algorithm approach. J. Comput. Chem. 1993, 14:1407-1414.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1407-1414
-
-
Judson, R.S.1
Jaeger, E.P.2
Treasurywala, A.M.3
Peterson, M.L.4
-
13
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley L.A., MacCallum R.M., Sternberg M.J.E. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 2000, 299:499-520.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Sternberg, M.J.E.3
-
14
-
-
0012638454
-
A genetic algorithm for conformational search of organic molecules: implications for materials chemistry
-
Keser M., Stupp S.I. A genetic algorithm for conformational search of organic molecules: implications for materials chemistry. Comput. Chem. 1998, 22:345-351.
-
(1998)
Comput. Chem.
, vol.22
, pp. 345-351
-
-
Keser, M.1
Stupp, S.I.2
-
15
-
-
0026210071
-
Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core
-
Lee C., Levitt M. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature 1991, 352:448-451.
-
(1991)
Nature
, vol.352
, pp. 448-451
-
-
Lee, C.1
Levitt, M.2
-
16
-
-
0026019108
-
Prediction of protein side-chain conformation by packing optimization
-
Lee C., Subbiah S. Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 1991, 217:373-388.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 373-388
-
-
Lee, C.1
Subbiah, S.2
-
18
-
-
50849118769
-
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection
-
Offman M.N., Tournier A.L., Bates P.A. Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct. Biol. 2008, 8.
-
(2008)
BMC Struct. Biol.
, pp. 8
-
-
Offman, M.N.1
Tournier, A.L.2
Bates, P.A.3
-
19
-
-
0018094892
-
Electrostatic effects in proteins
-
Perutz M.F. Electrostatic effects in proteins. Science 1978, 201:1187-1191.
-
(1978)
Science
, vol.201
, pp. 1187-1191
-
-
Perutz, M.F.1
-
20
-
-
0037412183
-
Protein design is NP-hard
-
Pierce N.A., Winfree E. Protein design is NP-hard. Protein Eng. 2002, 15:779-782.
-
(2002)
Protein Eng.
, vol.15
, pp. 779-782
-
-
Pierce, N.A.1
Winfree, E.2
-
22
-
-
0025283002
-
Electrostatic interactions in macromolecules - theory and applications
-
Sharp K.A., Honig B. Electrostatic interactions in macromolecules - theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19:301-332.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
23
-
-
77749258885
-
Adaptive niche radii and niche shapes approaches for niching with the CMA-ES
-
Shir O.M., Emmerich M., Back T. Adaptive niche radii and niche shapes approaches for niching with the CMA-ES. Evol. Comput. 2010, 18:97-126.
-
(2010)
Evol. Comput.
, vol.18
, pp. 97-126
-
-
Shir, O.M.1
Emmerich, M.2
Back, T.3
-
24
-
-
62749167980
-
MCCE2: Improving protein pK(a) calculations with extensive side chain rotamer sampling
-
Song Y.F., Mao J.J., Gunner M.R. MCCE2: Improving protein pK(a) calculations with extensive side chain rotamer sampling. J. Comput. Chem. 2009, 30:2231-2247.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2231-2247
-
-
Song, Y.F.1
Mao, J.J.2
Gunner, M.R.3
-
25
-
-
32144439339
-
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
-
Xie W., Sahinidis N.V. Residue-rotamer-reduction algorithm for the protein side-chain conformation problem. Bioinformatics 2006, 22:188-194.
-
(2006)
Bioinformatics
, vol.22
, pp. 188-194
-
-
Xie, W.1
Sahinidis, N.V.2
|