-
1
-
-
0029186289
-
TOPITS: Threading one-dimensional predictions into three-dimensional structures
-
Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T., Wodak, S., eds.: Cambridge, England, AAAI Press
-
Rost, B.: TOPITS: Threading one-dimensional predictions into three-dimensional structures. In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T., Wodak, S., eds.: Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, England, AAAI Press (1995) 314-321
-
(1995)
Third International Conference on Intelligent Systems for Molecular Biology
, pp. 314-321
-
-
Rost, B.1
-
2
-
-
0031750906
-
An efficient computational method for globally optimal threadings
-
Xu, Y., Xu, D., Uberbacher, E.: An efficient computational method for globally optimal threadings. Journal of Computational Biology 5 (1998) 597-614
-
(1998)
Journal of Computational Biology
, vol.5
, pp. 597-614
-
-
Xu, Y.1
Xu, D.2
Uberbacher, E.3
-
3
-
-
0142184275
-
PROSPECT II: Protein structure prediction method for genome-scale applications
-
Kim, D., Xu, D., Guo, J., Ellrott, K., Xu, Y.: PROSPECT II: Protein structure prediction method for genome-scale applications. Protein Engineering 16 (2003) 641-650
-
(2003)
Protein Engineering
, vol.16
, pp. 641-650
-
-
Kim, D.1
Xu, D.2
Guo, J.3
Ellrott, K.4
Xu, Y.5
-
4
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones, D.: GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology 287 (1999) 797-815
-
(1999)
Journal of Molecular Biology
, vol.287
, pp. 797-815
-
-
Jones, D.1
-
5
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley, L., MacCallum, R., Sternberg, M.: Enhanced genome annotation using structural profiles in the program 3D-PSSM. Journal of Molecular Biology 299 (2000) 499-520
-
(2000)
Journal of Molecular Biology
, vol.299
, pp. 499-520
-
-
Kelley, L.1
MacCallum, R.2
Sternberg, M.3
-
7
-
-
4143083332
-
Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
-
von Ohsen, N., Sommer, L, Zimmer, R., Lengauer, T.: Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20 (2004) 2228-35
-
(2004)
Bioinformatics
, vol.20
, pp. 2228-2235
-
-
Von Ohsen, N.1
Sommer, L.2
Zimmer, R.3
Lengauer, T.4
-
8
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J., Tom, L.B., Kenji, M.: FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. Journal of Molecular Biology 310 (2001) 243-257
-
(2001)
Journal of Molecular Biology
, vol.310
, pp. 243-257
-
-
Shi, J.1
Tom, L.B.2
Kenji, M.3
-
9
-
-
0028907515
-
A branch-and-bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions
-
IEEE Computer Society Press
-
Lathrop, R., Smith, T.: A branch-and-bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions. In: Proceedings of the 27th Hawaii International Conference on System Sciences, IEEE Computer Society Press (1994)
-
(1994)
Proceedings of the 27th Hawaii International Conference on System Sciences
-
-
Lathrop, R.1
Smith, T.2
-
10
-
-
0346967395
-
On the approximation of protein threading
-
Akutsu, T., Miyano, S.: On the approximation of protein threading. Theoretical Computer Science 210 (1999) 261-275
-
(1999)
Theoretical Computer Science
, vol.210
, pp. 261-275
-
-
Akutsu, T.1
Miyano, S.2
-
11
-
-
0034491129
-
Saturated BLAST: Detecting distant homology using automated multiple intermediate sequence BLAST search
-
Li, W., Pio, F., Pawlowski, K., Godzik, A.: Saturated BLAST: detecting distant homology using automated multiple intermediate sequence BLAST search. Bioinformatics 16 (2000) 1105-1110
-
(2000)
Bioinformatics
, vol.16
, pp. 1105-1110
-
-
Li, W.1
Pio, F.2
Pawlowski, K.3
Godzik, A.4
-
12
-
-
0024816521
-
Construction of side-chains in homology modelling: Application to the c-terminal lobe of rhizopuspepsin
-
Summers, N., Karplus, M.: Construction of side-chains in homology modelling: Application to the c-terminal lobe of rhizopuspepsin. Journal of Molecular Biology 210 (1989) 785-811
-
(1989)
Journal of Molecular Biology
, vol.210
, pp. 785-811
-
-
Summers, N.1
Karplus, M.2
-
13
-
-
0025978283
-
α trace: Application to model building and detection of coordinate errors
-
α trace: Application to model building and detection of coordinate errors. Journal of Molecular Biology 218 (1991) 183-194
-
(1991)
Journal of Molecular Biology
, vol.218
, pp. 183-194
-
-
Holm, L.1
Sander, C.2
-
14
-
-
0026589733
-
The dead-end elimination theorem and its use in protein side-chain positioning
-
Desmet, J., Maeyer, M.D., Hazes, B., Laster, I.: The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356 (1992) 539-542
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
Maeyer, M.D.2
Hazes, B.3
Laster, I.4
-
15
-
-
0036643430
-
Fast and accurate side-chain topology and energy refinement (faster) as a new method for protein structure optimization
-
Desmet, J., Spriet, J., Laster, I.: Fast and accurate side-chain topology and energy refinement (faster) as a new method for protein structure optimization. Protein: Structure, Function and Genetics 48 (2002) 31-43
-
(2002)
Protein: Structure, Function and Genetics
, vol.48
, pp. 31-43
-
-
Desmet, J.1
Spriet, J.2
Laster, I.3
-
16
-
-
0032613301
-
Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
-
Jr., R.D.: Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Protein: Structure, Function and Genetics 3 (1999) 81-87
-
(1999)
Protein: Structure, Function and Genetics
, vol.3
, pp. 81-87
-
-
D. Jr., R.1
-
17
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu, A., Shelenkov, A., Jr., R.D.: A graph-theory algorithm for rapid protein side-chain prediction. Protein Science 12 (2003) 2001-2014
-
(2003)
Protein Science
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.1
Shelenkov, A.2
D. Jr., R.3
-
18
-
-
0031794714
-
Determinants of side chain conformational preferences in protein structures
-
Samudrala, R., Moult, J.: Determinants of side chain conformational preferences in protein structures. Protein Engineering 11 (1998) 991-997
-
(1998)
Protein Engineering
, vol.11
, pp. 991-997
-
-
Samudrala, R.1
Moult, J.2
-
19
-
-
0035838974
-
Extending the accuracy limits of prediction for side-chain conformations
-
Xiang, Z., Honig, B.: Extending the accuracy limits of prediction for side-chain conformations. Journal of Molecular Biology 311 (2001) 421-430
-
(2001)
Journal of Molecular Biology
, vol.311
, pp. 421-430
-
-
Xiang, Z.1
Honig, B.2
-
20
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
Bower, M., Cohen, F., Jr., R.D.: Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. Journal of Molecular Biology 267 (1997) 1268-1282
-
(1997)
Journal of Molecular Biology
, vol.267
, pp. 1268-1282
-
-
Bower, M.1
Cohen, F.2
D. Jr., R.3
-
21
-
-
0036149564
-
Side-chain modelling with an optimized scoring function
-
Liang, S., Grishin, N.: side-chain modelling with an optimized scoring function. Protein Science 11 (2002) 322-331
-
(2002)
Protein Science
, vol.11
, pp. 322-331
-
-
Liang, S.1
Grishin, N.2
-
22
-
-
26444540963
-
Protein side-chain placement: Probabilistic inference and integer programming methods
-
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
-
Hong, E., Lozano-Perez, T.: Protein side-chain placement: probabilistic inference and integer programming methods. Technical report, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (2004)
-
(2004)
Technical Report
-
-
Hong, E.1
Lozano-Perez, T.2
-
23
-
-
10044241588
-
A semidefinite programming approach to side-chain positioning with new rounding strategies
-
Special Issue in Computational Molecular Biology/Bioinformatics
-
Chazelle, B., Kingsford, C., Singh, M.: A semidefinite programming approach to side-chain positioning with new rounding strategies. Informs Journal on Computing, Special Issue in Computational Molecular Biology/Bioinformatics (2004) 86-94
-
(2004)
Informs Journal on Computing
, pp. 86-94
-
-
Chazelle, B.1
Kingsford, C.2
Singh, M.3
-
24
-
-
26444543542
-
Solving and analyzing side-chain positioning problems using linear and integer programming
-
Kingsford, C.L., Chazelle, B., Singh, M.: Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics (2004)
-
(2004)
Bioinformatics
-
-
Kingsford, C.L.1
Chazelle, B.2
Singh, M.3
-
25
-
-
68549106477
-
Side chain-positioning as an integer programming problem
-
Springer-Verlag
-
Eriksson, O., Zhou, Y., Elofsson, A.: Side chain-positioning as an integer programming problem. In: Proceedings of the First International Workshop on Algorithms in Bioinformatics, Springer-Verlag (2001) 128-141
-
(2001)
Proceedings of the First International Workshop on Algorithms in Bioinformatics
, pp. 128-141
-
-
Eriksson, O.1
Zhou, Y.2
Elofsson, A.3
-
26
-
-
26444570554
-
Protein side-chain packing problem: A maximum common edge-weight clique algorithmic approach
-
Dukka, K., Tomita, E., Suzuki, J., Akutsu, T.: Protein side-chain packing problem: a maximum common edge-weight clique algorithmic approach. In: The Second Asia Pacific Bioinformatics Conference. (2004)
-
(2004)
The Second Asia Pacific Bioinformatics Conference
-
-
Dukka, K.1
Tomita, E.2
Suzuki, J.3
Akutsu, T.4
-
27
-
-
26444435050
-
A branch and cut algorithm for the optimal solution of the side-chain placement problem
-
Max-Planck-Institute für Informatik
-
Althaus, E., Kohlbacher, O., Lenhof, H., Müller, P.: A branch and cut algorithm for the optimal solution of the side-chain placement problem. Technical Report MPI-I-2000-1-001, Max-Planck-Institute für Informatik (2000)
-
(2000)
Technical Report
, vol.MPI-I-2000-1-001
-
-
Althaus, E.1
Kohlbacher, O.2
Lenhof, H.3
Müller, P.4
-
28
-
-
0027160197
-
Backbone-dependent rotamer library for proteins: Application to side-chain prediction
-
Jr., R.D., Karplus, M.: Backbone-dependent rotamer library for proteins: Application to side-chain prediction. Journal of Molecular Biology 230 (1993) 543-574
-
(1993)
Journal of Molecular Biology
, vol.230
, pp. 543-574
-
-
D. Jr., R.1
Karplus, M.2
-
30
-
-
14544303007
-
NP-hardness results for protein side-chain packing
-
Miyano, S., Takagi, T., eds.
-
Akutsu, T.: NP-hardness results for protein side-chain packing. In Miyano, S., Takagi, T., eds.: Genome Informatics 8. (1997) 180-186
-
(1997)
Genome Informatics
, vol.8
, pp. 180-186
-
-
Akutsu, T.1
-
31
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali, A., Blundell, T.: Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology (1993) 779-815
-
(1993)
Journal of Molecular Biology
, pp. 779-815
-
-
Sali, A.1
Blundell, T.2
-
32
-
-
0031717560
-
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
-
Leach, A., Lemon, A.: Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Protein: Structure, Function and Genetics 33 (1998) 227-239
-
(1998)
Protein: Structure, Function and Genetics
, vol.33
, pp. 227-239
-
-
Leach, A.1
Lemon, A.2
-
33
-
-
0028212927
-
Efficient rotamer elimination applied to protein side-chains and related spin glasses
-
Goldstein, R.: Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophysical Journal 66 (1994) 1335-1340
-
(1994)
Biophysical Journal
, vol.66
, pp. 1335-1340
-
-
Goldstein, R.1
-
34
-
-
0000673493
-
Graph minors. II. Algorithmic aspects of tree-width
-
Robertson, N., Seymour, P.: Graph minors. II. algorithmic aspects of tree-width. Journal of Algorithms 7 (1986) 309-322
-
(1986)
Journal of Algorithms
, vol.7
, pp. 309-322
-
-
Robertson, N.1
Seymour, P.2
-
35
-
-
26444443738
-
Solving frequency assignment problems via tree-decomposition
-
Maastricht: METEOR, Maastricht Research School of Economics of Technology and Organization
-
Koster, A., van Hoesel, S., Kolen, A.: Solving frequency assignment problems via tree-decomposition. Research Memoranda 036, Maastricht: METEOR, Maastricht Research School of Economics of Technology and Organization (1999) available at http://ideas.repec.org/p/dgr/umamet/1999036.html.
-
(1999)
Research Memoranda
, vol.36
-
-
Koster, A.1
Van Hoesel, S.2
Kolen, A.3
-
36
-
-
84899032200
-
Thin junction trees
-
Dietterich, T., Becker, S., Ghahramani, Z., eds.
-
Bach, F., Jordan, M.: Thin junction trees. In Dietterich, T., Becker, S., Ghahramani, Z., eds.: Advances in Neural Information Processing Systems (NIPS). Volume 14. (2002)
-
(2002)
Advances in Neural Information Processing Systems (NIPS)
, vol.14
-
-
Bach, F.1
Jordan, M.2
-
37
-
-
0000245736
-
Complexity of finding embedding in a k-tree
-
Arnborg, S., Corneil, D., Proskurowski, A.: Complexity of finding embedding in a k-tree. SIAM Journal on Algebraic and Discrete Methods 8 (1987) 277-284
-
(1987)
SIAM Journal on Algebraic and Discrete Methods
, vol.8
, pp. 277-284
-
-
Arnborg, S.1
Corneil, D.2
Proskurowski, A.3
-
38
-
-
0030703027
-
Separators for sphere-packings and nearest neighbor graphs
-
Miller, G.L., Teng, S., Thurston, W., Vavasis, S.A.: Separators for sphere-packings and nearest neighbor graphs. Journal of ACM 44 (1997) 1-29
-
(1997)
Journal of ACM
, vol.44
, pp. 1-29
-
-
Miller, G.L.1
Teng, S.2
Thurston, W.3
Vavasis, S.A.4
-
39
-
-
0344392004
-
The minimum degree heuristic and the minimal triangulation process
-
Lecture Notes in Computer Science, Springer Verlag
-
Berry, A., Heggernes, P., Simonet, G.: The minimum degree heuristic and the minimal triangulation process. Volume 2880., Proceedings WG 2003 - 29th Workshop on Graph Theoretic Concepts in Computer Science, Lecture Notes in Computer Science, Springer Verlag (2003) 58-70
-
(2003)
Proceedings WG 2003 - 29th Workshop on Graph Theoretic Concepts in Computer Science
, vol.2880
, pp. 58-70
-
-
Berry, A.1
Heggernes, P.2
Simonet, G.3
-
40
-
-
0033665510
-
BALL - Rapid software prototyping in computational molecular biology
-
Kohlbacher, O., Lenhof, H.: BALL - rapid software prototyping in computational molecular biology. Bioinformatics 16 (2000) 815C824
-
(2000)
Bioinformatics
, vol.16
-
-
Kohlbacher, O.1
Lenhof, H.2
-
41
-
-
0032201716
-
An optimal algorithm for approximate nearest neighbor searching in fixed dimensions
-
Arya, S., Mount, D., Netanyahu, N., Silverman, R., Wu, A.: An optimal algorithm for approximate nearest neighbor searching in fixed dimensions. Journal of ACM 45 (1998) 891-923
-
(1998)
Journal of ACM
, vol.45
, pp. 891-923
-
-
Arya, S.1
Mount, D.2
Netanyahu, N.3
Silverman, R.4
Wu, A.5
-
44
-
-
0037731050
-
Protein threading by linear programming
-
Hawaii, USA
-
Xu, J., Li, M., Lin, G., Kim, D., Xu, Y.: Protein threading by linear programming. In: Biocomputing: Proceedings of the 2003 Pacific Symposium, Hawaii, USA (2003) 264-275
-
(2003)
Biocomputing: Proceedings of the 2003 Pacific Symposium
, pp. 264-275
-
-
Xu, J.1
Li, M.2
Lin, G.3
Kim, D.4
Xu, Y.5
-
45
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
Xu, J., Li, M., Kim, D., Xu, Y.: RAPTOR: optimal protein threading by linear programming. Journal of Bioinformatics and Computational Biology 1 (2003) 95-117
-
(2003)
Journal of Bioinformatics and Computational Biology
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
|