-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science. 181:223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0034604105
-
A surprising simplicity to protein folding
-
Baker, D. 2000. A surprising simplicity to protein folding. Nature. 405:39-42.
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
3
-
-
0025935158
-
Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: A prediction of the structure of the catalytic domain of protein kinases
-
Benner, S. A., and D. Gerloff. 1991. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. Adv. Enzyme Regul. 31:121-181.
-
(1991)
Adv. Enzyme Regul.
, vol.31
, pp. 121-181
-
-
Benner, S.A.1
Gerloff, D.2
-
4
-
-
0033954256
-
The protein data bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 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
-
5
-
-
0000467663
-
Finding the needle in a haystack: Educing native folds from ambiguous ab initial protein structure predictions
-
Betancourt, M. R., and J. Skolnick. 2001. Finding the needle in a haystack: educing native folds from ambiguous ab initial protein structure predictions. J. Comput. Chem. 22:339-353.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 339-353
-
-
Betancourt, M.R.1
Skolnick, J.2
-
6
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J. U., R. Luthy, and D. Eisenberg. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
8
-
-
0031473847
-
SWISS-MODEL and the Swiss-Pdb-Viewer: An environment for comparative protein modeling
-
Guex, N., and M. C. Peitsch. 1997. SWISS-MODEL and the Swiss-Pdb-Viewer: an environment for comparative protein modeling. Electrophoresis. 18:2714-23.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
9
-
-
0000448982
-
Prediction of protein antigenic determinants from amino acid sequences
-
Hopp, T. P., and K. R. Woods. 1981. Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. USA. 78:3824-3828.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 3824-3828
-
-
Hopp, T.P.1
Woods, K.R.2
-
11
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
12
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
13
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus, K., C. Barrett, and R. Hughey. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics. 14:846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
14
-
-
0035964191
-
TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
-
Epub 2001 Aug 14
-
Kihara, D., H. Lu, A. Kolinski, and J. Skolnick. 2001. TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. USA. 98:10125-10130. Epub 2001 Aug 14.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10125-10130
-
-
Kihara, D.1
Lu, H.2
Kolinski, A.3
Skolnick, J.4
-
15
-
-
0035427225
-
Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
-
Kolinski, A., M. R. Betancourt, D. Kihara, P. Rotkiewicz, and J. Skolnick. 2001. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins. 44:133-149.
-
(2001)
Proteins
, vol.44
, pp. 133-149
-
-
Kolinski, A.1
Betancourt, M.R.2
Kihara, D.3
Rotkiewicz, P.4
Skolnick, J.5
-
16
-
-
0001179396
-
An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass
-
Kolinski, A., L. Jaroszewski, P. Rotkiewicz, and J. Skolnick. 1998. An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass. J. Chem. Phys. B. 102:4628-4637.
-
(1998)
J. Chem. Phys. B
, vol.102
, pp. 4628-4637
-
-
Kolinski, A.1
Jaroszewski, L.2
Rotkiewicz, P.3
Skolnick, J.4
-
17
-
-
0028203492
-
Monte Carlo simulations of protein folding: I. Lattice model and interaction scheme
-
Kolinski, A., and J. Skolnick. 1994. Monte Carlo simulations of protein folding: I. lattice model and interaction scheme. Proteins. 18:338-352.
-
(1994)
Proteins
, vol.18
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
18
-
-
0031855094
-
Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
-
Kolinski, A., and J. Skolnick. 1998. Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32:475-494.
-
(1998)
Proteins
, vol.32
, pp. 475-494
-
-
Kolinski, A.1
Skolnick, J.2
-
19
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
20
-
-
12444291079
-
TOUCHSTONEX: Protein structure prediction using sparse NMR data
-
In press
-
Li, W., Y. Zhang, D. Kihara, Y. Huang, D. Zheng, G. Montelione, A. Kolinski, and J. Skolnick. 2002. TOUCHSTONEX: Protein structure prediction using sparse NMR data. Proteins. In press.
-
(2002)
Proteins
-
-
Li, W.1
Zhang, Y.2
Kihara, D.3
Huang, Y.4
Zheng, D.5
Montelione, G.6
Kolinski, A.7
Skolnick, J.8
-
21
-
-
0035150828
-
Progress in protein structure prediction
-
Murzin, A. G. 2001. Progress in protein structure prediction. Nat. Struct. Biol. 8:110-112.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 110-112
-
-
Murzin, A.G.1
-
23
-
-
0034628922
-
Combination of threading potentials and sequence profiles improves fold recognition
-
Panchenko, A. R., A. Marchler-Bauer, and S. H. Bryant. 2000. Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296:1319-1331.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1319-1331
-
-
Panchenko, A.R.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
24
-
-
0035956886
-
Recent improvements in prediction of protein structure by global optimization of a potential energy function
-
Pillardy, J., C. Czaplewski, A. Liwo, J. Lee, D. R. Ripoll, R. Kazmierkiewicz, S. Oldziej, W. J. Wedemeyer, K. D. Gibson, Y. A. Arnautova, J. Saunders, Y. J. Ye, and H. A. Scheraga. 2001. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA. 98:2329-2333.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 2329-2333
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Lee, J.4
Ripoll, D.R.5
Kazmierkiewicz, R.6
Oldziej, S.7
Wedemeyer, W.J.8
Gibson, K.D.9
Arnautova, Y.A.10
Saunders, J.11
Ye, Y.J.12
Scheraga, H.A.13
-
25
-
-
0028300741
-
Combining evolutionary information and neural network to predict protein secondary structure
-
Rost, B., and C. Sander. 1994. Combining evolutionary information and neural network to predict protein secondary structure. Proteins. 19:55-77.
-
(1994)
Proteins
, vol.19
, pp. 55-77
-
-
Rost, B.1
Sander, C.2
-
26
-
-
0031307019
-
Evaluation of comparative protein structure modeling by MODELLER-3
-
Sanchez, R., and A. Sali. 1997. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins. (Suppl. 1):50-58.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 50-58
-
-
Sanchez, R.1
Sali, A.2
-
27
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J. E., and C. L. Brooks, III. 2001. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:499-535.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.E.1
Brooks C.L. III2
-
28
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of smaller proteins
-
Shortle, D., K. T. Simons, and D. Baker. 1998. Clustering of low-energy conformations near the native structures of smaller proteins. Proc. Natl. Acad. Sci. USA. 95:11158-11162.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
29
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-dependent and sequence-independent features of proteins
-
Simons, K. T., I. Ruczinski, C. Kooperberg, B. A. Fox, C. Bystroff, and D. Baker. 1999. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-dependent and sequence-independent features of proteins. Proteins. 34:82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
30
-
-
0035830958
-
Prospects for ab initio protein structural genomics
-
Simons, K. T., C. Strauss, and D. Baker. 2001. Prospects for ab initio protein structural genomics. J. Mol. Biol. 306:1191-1199.
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 1191-1199
-
-
Simons, K.T.1
Strauss, C.2
Baker, D.3
-
31
-
-
0030983768
-
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
-
Skolnick, J., L. Jaroszewski, A. Kolinski, and A. Godzik. 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 6:676-688.
-
(1997)
Protein Sci.
, vol.6
, pp. 676-688
-
-
Skolnick, J.1
Jaroszewski, L.2
Kolinski, A.3
Godzik, A.4
-
32
-
-
0035866002
-
Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
-
Skolnick, J., and D. Kihara. 2001. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins. 42:319-331.
-
(2001)
Proteins
, vol.42
, pp. 319-331
-
-
Skolnick, J.1
Kihara, D.2
-
33
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
Tobi, D., and R. Elber. 2000. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins. 41:40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
34
-
-
0034141931
-
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
-
Vendruscolo, M., R. Najmanovich, and E. Domany. 1999. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins. 38:134-148.
-
(1999)
Proteins
, vol.38
, pp. 134-148
-
-
Vendruscolo, M.1
Najmanovich, R.2
Domany, E.3
-
35
-
-
0036681386
-
Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
-
Zhang, Y., D. Kihara, and J. Skolnick. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48:192-201.
-
(2002)
Proteins
, vol.48
, pp. 192-201
-
-
Zhang, Y.1
Kihara, D.2
Skolnick, J.3
-
36
-
-
0034901419
-
Stretching single-stranded DNA: Interplay of electrostatic, base-paring, and base-pair stacking interactions
-
Zhang, Y., H. J. Zhou, and Z. C. Ouyang. 2001. Stretching single-stranded DNA: interplay of electrostatic, base-paring, and base-pair stacking interactions. Biophys. J. 81:1133-1143.
-
(2001)
Biophys. J.
, vol.81
, pp. 1133-1143
-
-
Zhang, Y.1
Zhou, H.J.2
Ouyang, Z.C.3
|