-
1
-
-
0035702809
-
Critical assessment of methods of protein structure prediction (CASP): Round IV
-
Moult,J., Fidelis,K., Zemla,A. and Hubbard,T. (2001) Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins, 45 (Suppl. 5), 2-7.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 2-7
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
Hubbard, T.4
-
2
-
-
0035698589
-
CAFASP2: The second critical assessment of fully automated structure prediction methods
-
Fischer,D., Elofsson,A., Rychlewski,L., Pazos,F., Valencia,A., Rost,B., Ortiz,A.R. and Dunbrack,R.L.,Jr (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins, 45 (Suppl. 5), 171-183.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 171-183
-
-
Fischer, D.1
Elofsson, A.2
Rychlewski, L.3
Pazos, F.4
Valencia, A.5
Rost, B.6
Ortiz, A.R.7
Dunbrack Jr., R.L.8
-
3
-
-
0035698724
-
LiveBench-2: Large-scale automated evaluation of protein structure prediction servers
-
Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins, 45, 184-191.
-
(2001)
Proteins
, vol.45
, pp. 184-191
-
-
Bujnicki, J.M.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
4
-
-
0036139410
-
EVA: Continuous automatic evaluation of protein structure prediction servers
-
Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Fiser,A., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.
-
(2001)
Bioinformatics
, vol.17
, pp. 1242-1243
-
-
Eyrich, V.A.1
Marti-Renom, M.A.2
Przybylski, D.3
Madhusudhan, M.S.4
Fiser, A.5
Pazos, F.6
Valencia, A.7
Sali, A.8
Rost, B.9
-
5
-
-
0035755109
-
Assessment of the CASP4 fold recognition category
-
Sippl,M.J., Lackner,P., Domingues,F.S., Prlic,A., Malik,R., Andreeva,A. and Wiederstein,M. (2001) Assessment of the CASP4 fold recognition category. Proteins, 45 (Suppl. 5), 55-67.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 55-67
-
-
Sippl, M.J.1
Lackner, P.2
Domingues, F.S.3
Prlic, A.4
Malik, R.5
Andreeva, A.6
Wiederstein, M.7
-
6
-
-
0034663597
-
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
-
Cuff,J.A. and Barton,G.J. (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
-
(2000)
Proteins
, vol.40
, pp. 502-511
-
-
Cuff, J.A.1
Barton, G.J.2
-
7
-
-
0035748718
-
Sequence-structure homology recognition by iterative alignment refinement and comparative modeling
-
Williams,M.G., Shirai,H., Shi,J., Nagendra,H.G., Mueller,J., Mizuguchi,K., Miguel,R.N., Innis,C.A., Deane,C.M., Chen,L. et al. (2001) Sequence-structure homology recognition by iterative alignment refinement and comparative modeling. Proteins, 45 (Suppl. 5), 92-97.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 92-97
-
-
Williams, M.G.1
Shirai, H.2
Shi, J.3
Nagendra, H.G.4
Mueller, J.5
Mizuguchi, K.6
Miguel, R.N.7
Innis, C.A.8
Deane, C.M.9
Chen, L.10
-
8
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
9
-
-
0242362160
-
A 'Frankenstein's monster' approach to comparative modeling: Merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation
-
In press
-
Kosinski, J., Cymerman, I.A., Feder, M., Kurowski, M.A., Sasin, J.M. and Bujnicki,J.M. (2003) A 'Frankenstein's monster' approach to comparative modeling: merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation. Proteins, in press.
-
(2003)
Proteins
-
-
Kosinski, J.1
Cymerman, I.A.2
Feder, M.3
Kurowski, M.A.4
Sasin, J.M.5
Bujnicki, J.M.6
-
10
-
-
0035703311
-
Analysis and assessment of comparative modeling predictions in CASP4
-
Tramontano,A., Leplae,R. and Morea,V. (2001) Analysis and assessment of comparative modeling predictions in CASP4. Proteins, 45 (Suppl. 5), 22-38.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 22-38
-
-
Tramontano, A.1
Leplae, R.2
Morea, V.3
-
11
-
-
0034853120
-
Structure prediction Meta Server
-
Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) Structure prediction Meta Server. Bioinformatics, 17, 750-751.
-
(2001)
Bioinformatics
, vol.17
, pp. 750-751
-
-
Bujnicki, J.M.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
12
-
-
0037251964
-
The InterPro Database, 2003 brings increased coverage and new features
-
Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Barrell,D., Bateman,A., Binns,D., Biswas,M., Bradley,P., Bork,P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 315-318
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Barrell, D.5
Bateman, A.6
Binns, D.7
Biswas, M.8
Bradley, P.9
Bork, P.10
-
13
-
-
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
-
14
-
-
0035748354
-
What is the value added by human intervention in protein structure prediction?
-
Karplus,K., Karchin,R., Barrett,C., Tu,S., Cline,M., Diekhans,M., Grate,L., Casper,J. and Hughey,R. (2001) What is the value added by human intervention in protein structure prediction? Proteins, 45 (Suppl. 5), 86-91.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 86-91
-
-
Karplus, K.1
Karchin, R.2
Barrett, C.3
Tu, S.4
Cline, M.5
Diekhans, M.6
Grate, L.7
Casper, J.8
Hughey, R.9
-
15
-
-
0033933636
-
Cascaded multiple classifiers for secondary structure prediction
-
Ouali,M. and King,R.D. (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Sci., 9, 1162-1176.
-
(2000)
Protein Sci.
, vol.9
, pp. 1162-1176
-
-
Ouali, M.1
King, R.D.2
-
16
-
-
0028211273
-
A model recognition approach to the prediction of all-helical membrane protein structure and topology
-
Jones,D.T., Taylor,W.R. and Thornton,J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 33, 3038-3049.
-
(1994)
Biochemistry
, vol.33
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
17
-
-
0031614678
-
A hidden Markov model for predicting transmembrane helices in protein sequences
-
Sonnhammer,E.L., von Heijne,G. and Krogh,A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.6
, pp. 175-182
-
-
Sonnhammer, E.L.1
von Heijne, G.2
Krogh, A.3
-
18
-
-
0000207681
-
TMbase - A database of membrane spanning proteins segments
-
Hofmann,K. and Stoffel,W. (1993) TMbase - a database of membrane spanning proteins segments. Biol. Chem., 374, 166
-
(1993)
Biol. Chem.
, vol.374
, pp. 166
-
-
Hofmann, K.1
Stoffel, W.2
-
19
-
-
0037248878
-
The Protein Data Bank and structural genomics
-
Westbrook,J., Feng,Z., Chen,L., Yang,H. and Berman,H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489-491.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 489-491
-
-
Westbrook, J.1
Feng, Z.2
Chen, L.3
Yang, H.4
Berman, H.M.5
-
20
-
-
0037731050
-
Protein structure prediction by linear programming
-
Xu,J., Li,M., Lin,G., Kim,D. and Xu,Y. (2003) Protein structure prediction by linear programming. Pac. Symp. Biocomput., 264-275.
-
(2003)
Pac. Symp. Biocomput.
, pp. 264-275
-
-
Xu, J.1
Li, M.2
Lin, G.3
Kim, D.4
Xu, Y.5
-
21
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley,L.A., McCallum,C.M. and Sternberg,M.J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299, 501-522.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 501-522
-
-
Kelley, L.A.1
McCallum, C.M.2
Sternberg, M.J.3
-
22
-
-
0035967880
-
Fugue: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) Fugue: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
23
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones,D.T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287, 797-815.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
24
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
-
(2000)
Protein Sci.
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.3
Godzik, A.4
-
25
-
-
0033654768
-
Hybrid fold recognition: Combining sequence derived properties with evolutionary information
-
Fischer,D. (2000) Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac. Symp. Biocomput., 119-130.
-
(2000)
Pac. Symp. Biocomput.
, pp. 119-130
-
-
Fischer, D.1
-
26
-
-
0034780030
-
Pcons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom,J., Rychlewski,L., Bujnicki,J.M. and Elofsson,A. (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci., 10, 2354-2362.
-
(2001)
Protein Sci.
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
Rychlewski, L.2
Bujnicki, J.M.3
Elofsson, A.4
-
27
-
-
0032613301
-
Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
-
Dunbrack,R.L. (1999) Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Proteins (Suppl. 3), 81-87.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 81-87
-
-
Dunbrack, R.L.1
-
28
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy,R., Bowie,J.U. and Eisenberg,D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
|