-
1
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu, A.A., Shelenkov, A.A., and Dunbrack, Jr., R.L. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12, 2001-2014.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack Jr., R.L.3
-
2
-
-
33846603216
-
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design
-
Dantas, G., Corrent, C., Reichow, S.L., et al. 2007. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Biol. 366, 1209-1221.
-
(2007)
J. Mol. Biol
, vol.366
, pp. 1209-1221
-
-
Dantas, G.1
Corrent, C.2
Reichow, S.L.3
-
3
-
-
0026589733
-
The dead-end elmination theorem and its use in protein side-chain positioning
-
Desmet, J., Maeyer, M.D., Hazes, B., et al. 1992. The dead-end elmination theorem and its use in protein side-chain positioning. Nature 356, 539-542.
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
Maeyer, M.D.2
Hazes, B.3
-
4
-
-
0027160197
-
Back-bone dependent rotamer library for proteins: Application to side-chain prediction
-
Dunbrack, Jr., R.L., and Karplus, M. 1993. Back-bone 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 Jr., R.L.1
Karplus, M.2
-
6
-
-
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
-
7
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray, J.J., Moughon, S., Wang, C., et al. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331, 281-299.
-
(2003)
J. Mol. Biol
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
-
8
-
-
33745185781
-
Hidden conditional random fields for phone classification
-
pgs
-
Gunawardana, A., Mahajan, M., Acero, A., et al. 2005. Hidden conditional random fields for phone classification. INTERSPEECH, pgs. 1117-1120.
-
(2005)
INTERSPEECH
, pp. 1117-1120
-
-
Gunawardana, A.1
Mahajan, M.2
Acero, A.3
-
9
-
-
16344382546
-
Solving and analyzing side-chain positioning problems using linear and integer programming
-
Kingsford, C.L., Chazelle, B., and Singh, M. 2005. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21, 1028-1039.
-
(2005)
Bioinformatics
, vol.21
, pp. 1028-1039
-
-
Kingsford, C.L.1
Chazelle, B.2
Singh, M.3
-
10
-
-
33745842499
-
Convergent tree-reweighted message passing for energy minimization
-
Kolmogorov, V. 2005. Convergent tree-reweighted message passing for energy minimization. Proc. AI Stats, 182-189.
-
(2005)
Proc. AI Stats
, pp. 182-189
-
-
Kolmogorov, V.1
-
12
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme, T., Morozov, A.V., and Baker, D. 2003. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326, 1239-1259.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
13
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman, B., and Baker, D. 2000. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. USA 97, 10383-10388.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
14
-
-
0142192295
-
Conditional random fields: Probabilistic models for segmenting and labeling sequence data
-
Lafferty, J., McCallum, A., and Pereira, F. 2001. Conditional random fields: probabilistic models for segmenting and labeling sequence data. ICML 282-289.
-
(2001)
ICML
, pp. 282-289
-
-
Lafferty, J.1
McCallum, A.2
Pereira, F.3
-
15
-
-
33646426783
-
Kernel conditional random fields: Representation and clique selection
-
Lafferty, J., Zhu, X., and Liu, Y. 2004. Kernel conditional random fields: representation and clique selection. ICML, 64-71.
-
(2004)
ICML
, pp. 64-71
-
-
Lafferty, J.1
Zhu, X.2
Liu, Y.3
-
16
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis, T., and Karplus, M. 1999. Effective energy function for proteins in solution. Proteins 35, 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
17
-
-
15944389004
-
An adaptive dynamic programming algorithm for the side chain placement problem
-
Leaver-Fay, A., Kuhlman, B., and Snoeyink, J. 2005. An adaptive dynamic programming algorithm for the side chain placement problem. Pac. Symp. Biocomput. 10, 16-27.
-
(2005)
Pac. Symp. Biocomput
, vol.10
, pp. 16-27
-
-
Leaver-Fay, A.1
Kuhlman, B.2
Snoeyink, J.3
-
18
-
-
84862617580
-
Loss functions for discriminative training of energy-based models
-
LeCun, Y., and Huang, F. 2005. Loss functions for discriminative training of energy-based models. Proc. AIStats'05, 206-213.
-
(2005)
Proc. AIStats'05
, pp. 206-213
-
-
LeCun, Y.1
Huang, F.2
-
19
-
-
33747859373
-
Rosettadesign server for protein design
-
Liu, Y., and Kuhlman, B. 2006. Rosettadesign server for protein design. NAR 34, W235-W238.
-
(2006)
NAR
, vol.34
-
-
Liu, Y.1
Kuhlman, B.2
-
20
-
-
33745933877
-
Globally optimal solutions for energy minimization in stereo vision using reweighted belief propagation
-
Meltzer, T., Yanover, C., and Weiss, Y. 2005. Globally optimal solutions for energy minimization in stereo vision using reweighted belief propagation. Proc. ICCV, 428-435.
-
(2005)
Proc. ICCV
, pp. 428-435
-
-
Meltzer, T.1
Yanover, C.2
Weiss, Y.3
-
22
-
-
1342310514
-
Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library
-
Peterson, R.W., Dutton, P.L., and Wand, A.J. 2004. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. Protein Sci. 13, 735-751.
-
(2004)
Protein Sci
, vol.13
, pp. 735-751
-
-
Peterson, R.W.1
Dutton, P.L.2
Wand, A.J.3
-
23
-
-
0001114311
-
Conformational splitting: A more powerful criterion for dead-end elimination
-
Pierce, N.A., Spriet, J.A., Desmet, J., et al. 2000. Conformational splitting: A more powerful criterion for dead-end elimination. J. Comput. Chem. 21, 999-1009.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 999-1009
-
-
Pierce, N.A.1
Spriet, J.A.2
Desmet, J.3
-
24
-
-
33749253818
-
Conditional random fields for object recognition
-
S. Thrun, L. Saul, and B. Schölkopf eds, MIT Press, Cambridge, MA
-
Quattoni, A., Collins, M., and Darrell, T. 2005. Conditional random fields for object recognition. In: S. Thrun, L. Saul, and B. Schölkopf (eds.), Advances in Neural Information Processing Systems 17. MIT Press, Cambridge, MA, 1097-1104.
-
(2005)
Advances in Neural Information Processing Systems 17
, pp. 1097-1104
-
-
Quattoni, A.1
Collins, M.2
Darrell, T.3
-
25
-
-
2442449534
-
Modeling structurally variable regions in homologous proteins with Rosetta
-
Rohl, C.A., Strauss, C.E.M., Chivian, D., et al. 2004. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55, 656-677.
-
(2004)
Proteins
, vol.55
, pp. 656-677
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Chivian, D.3
-
26
-
-
84898948585
-
Max-margin markov networks
-
S. Thrun, L. Saul, and B. Schölkopf eds, MIT Press, Cambridge, MA
-
Taskar, B., Guestrin, C., and Koller, D. 2004. Max-margin markov networks. In: S. Thrun, L. Saul, and B. Schölkopf (eds.), Advances in Neural Information Processing Systems 16. MIT Press, Cambridge, MA, 25-32.
-
(2004)
Advances in Neural Information Processing Systems 16
, pp. 25-32
-
-
Taskar, B.1
Guestrin, C.2
Koller, D.3
-
27
-
-
33749243756
-
Accelerated training of conditional random fields with stochastic meta-descent
-
Vishwanathan, S., Schraudolph, N., Schmidt, M., et al. 2006. Accelerated training of conditional random fields with stochastic meta-descent. ICML, 969-976.
-
(2006)
ICML
, pp. 969-976
-
-
Vishwanathan, S.1
Schraudolph, N.2
Schmidt, M.3
-
28
-
-
27744456278
-
MAP estimation via agreement on (hyper)trees: Message-passing and linear-programming approaches
-
Wainwright, M.J., Jaakkola, T., and Willsky, A.S. 2005. MAP estimation via agreement on (hyper)trees: message-passing and linear-programming approaches. IEEE Trans. Inform. Theory 51, 3697-3717.
-
(2005)
IEEE Trans. Inform. Theory
, vol.51
, pp. 3697-3717
-
-
Wainwright, M.J.1
Jaakkola, T.2
Willsky, A.S.3
-
29
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang, C., Schueler-Furman, O., and Baker, D. 2005. Improved side-chain modeling for protein-protein docking. Protein Sci. 14, 1328-1339.
-
(2005)
Protein Sci
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
31
-
-
33745778496
-
Linear programming relaxations and belief propagation - an empirical study
-
Yanover, C., Meltzer, T., and Weiss, Y. 2006. Linear programming relaxations and belief propagation - an empirical study. J. Mach. Learning Res. 7, 1887-1907.
-
(2006)
J. Mach. Learning Res
, vol.7
, pp. 1887-1907
-
-
Yanover, C.1
Meltzer, T.2
Weiss, Y.3
|