-
1
-
-
0036467068
-
Alignments grow, secondary structure prediction improves
-
Przybylski,D. and Rost,B. (2002) Alignments grow, secondary structure prediction improves. Proteins, 46, 197-205.
-
(2002)
Proteins
, vol.46
, pp. 197-205
-
-
Przybylski, D.1
Rost, B.2
-
2
-
-
26444473604
-
Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
-
Garg,A., Kaur,H. and Raghava,G.P. (2005) Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure. Proteins, 61, 318-324.
-
(2005)
Proteins
, vol.61
, pp. 318-324
-
-
Garg, A.1
Kaur, H.2
Raghava, G.P.3
-
3
-
-
14544299774
-
Optimizing long intrinsic disorder predictors with protein evolutionary information
-
Peng,K., Vucetic,S., Radivojac,P., Brown,C.J., Dunker,A.K. and Obradovic,Z. (2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. Comput. Biol., 3, 35-60.
-
(2005)
J. Bioinform. Comput. Biol.
, vol.3
, pp. 35-60
-
-
Peng, K.1
Vucetic, S.2
Radivojac, P.3
Brown, C.J.4
Dunker, A.K.5
Obradovic, Z.6
-
4
-
-
3042579686
-
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
-
Viklund,H. and Elofsson,A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci., 13, 1908-1917.
-
(2004)
Protein Sci.
, vol.13
, pp. 1908-1917
-
-
Viklund, H.1
Elofsson, A.2
-
5
-
-
21444454088
-
PROFcon: Novel prediction of long-range contacts
-
Punta,M. and Rost,B. (2005) PROFcon: novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
-
(2005)
Bioinformatics
, vol.21
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
6
-
-
19544369864
-
An evolution based classifier for prediction of protein interfaces without using protein structures
-
Res,I., Mihalek,I. and Lichtarge,O. (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics, 21, 2496-2501.
-
(2005)
Bioinformatics
, vol.21
, pp. 2496-2501
-
-
Res, I.1
Mihalek, I.2
Lichtarge, O.3
-
7
-
-
0344118117
-
Better prediction of sub-cellular localization by combining evolutionary and structural information
-
Nair,R. and Rost,B. (2003) Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins, 53, 917-930.
-
(2003)
Proteins
, vol.53
, pp. 917-930
-
-
Nair, R.1
Rost, B.2
-
8
-
-
33747825122
-
HHrep: De novo protein repeat detection and the origin of TIM barrels
-
Söding,J., Remmert,M., Biegert,A. and Lupas,A. (2006) HHrep: de novo protein repeat detection and the origin of TIM barrels. Nucleic Acids Res.
-
(2006)
Nucleic Acids Res.
-
-
Söding, J.1
Remmert, M.2
Biegert, A.3
Lupas, A.4
-
9
-
-
0036387236
-
Evaluation of structural and evolutionary contributions to deleterious mutation prediction
-
Saunders,C.T. and Baker,D. (2002) Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J. Mol. Biol., 322, 891-901.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 891-901
-
-
Saunders, C.T.1
Baker, D.2
-
10
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge,O., Bourne,H.R. and Cohen,F.E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
11
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli,S.S. and Russell,R.B. (2000) Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol., 303, 61-76.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
12
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
delSol Mesa,A., Pazos,F. and Valencia,A. (2003) Automatic methods for predicting functionally important residues. J. Mol. Biol., 326, 1289-1302.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1289-1302
-
-
delSol Mesa, A.1
Pazos, F.2
Valencia, A.3
-
13
-
-
29144462537
-
In silico identification of functional regions in proteins
-
Nimrod,G., Glaser,F., Steinberg,D., Ben-Tal,N. and Pupko,T. (2005) In silico identification of functional regions in proteins. Bioinformatics, 21, i328.
-
(2005)
Bioinformatics
, vol.21
-
-
Nimrod, G.1
Glaser, F.2
Steinberg, D.3
Ben-Tal, N.4
Pupko, T.5
-
14
-
-
0345827718
-
Using evolutionary information for the query and target improves fold recognition
-
Wallner,B., Fang,H., Ohlson,T., Frey-Skott,J. and Elofsson,A. (2004) Using evolutionary information for the query and target improves fold recognition. Proteins, 54, 342-350.
-
(2004)
Proteins
, vol.54
, pp. 342-350
-
-
Wallner, B.1
Fang, H.2
Ohlson, T.3
Frey-Skott, J.4
Elofsson, A.5
-
15
-
-
2342423130
-
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
-
Sadreyev,R.I. and Grishin,N.V. (2004) Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics, 20, 818-828.
-
(2004)
Bioinformatics
, vol.20
, pp. 818-828
-
-
Sadreyev, R.I.1
Grishin, N.V.2
-
16
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (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
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
17
-
-
0028181441
-
Hidden Markov models in computational biology. Applications to protein modeling
-
Krogh,A., Brown,M., Mian,I.S., Sjolander,K. and Haussler,D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
18
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 349-354
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
19
-
-
0031762837
-
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
-
Gerstein,M. (1998) Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics, 14, 707-714.
-
(1998)
Bioinformatics
, vol.14
, pp. 707-714
-
-
Gerstein, M.1
-
20
-
-
0034491129
-
Saturated BLAST: An automated multiple intermediate sequence search used to detect distant homology
-
Li,W., Pio,F., Pawlowski,K. and Godzik,A. (2000) Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics, 16, 1105-1110.
-
(2000)
Bioinformatics
, vol.16
, pp. 1105-1110
-
-
Li, W.1
Pio, F.2
Pawlowski, K.3
Godzik, A.4
-
21
-
-
25444458541
-
PSI-BLAST-ISS: An intermediate sequence search tool for estimation of the position-specific alignment reliability
-
Margelevicius,M. and Venclovas,C. (2005) PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC. Bioinformatics, 6, 185.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 185
-
-
Margelevicius, M.1
Venclovas, C.2
-
22
-
-
0036699189
-
Sequence clustering strategies improve remote homology recognitions while reducing search times
-
Li,W., Jaroszewski,L. and Godzik,A. (2002) Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein. Eng., 15, 643-649.
-
(2002)
Protein. Eng.
, vol.15
, pp. 643-649
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
23
-
-
27844519262
-
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins
-
Sandhya,S., Chakrabarti,S., Abhinandan,K.R., Sowdhamini,R. and Srinivasan,N. (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. J. Biomol. Struct. Dyn., 23, 283-298.
-
(2005)
J. Biomol. Struct. Dyn.
, vol.23
, pp. 283-298
-
-
Sandhya, S.1
Chakrabarti, S.2
Abhinandan, K.R.3
Sowdhamini, R.4
Srinivasan, N.5
-
24
-
-
0036111244
-
Fold recognition without folds
-
Koretke,K.K., Russell,R.B. and Lupas,A.N. (2002) Fold recognition without folds. Protein Sci., 11, 1575-1579.
-
(2002)
Protein Sci.
, vol.11
, pp. 1575-1579
-
-
Koretke, K.K.1
Russell, R.B.2
Lupas, A.N.3
-
25
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
26
-
-
20444422946
-
AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels
-
Coles,M., Djuranovic,S., Söding,J., Frickey,T., Koretke,K., Truffault,V., Martin,J. and Lupas,A.N. (2005) AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels. Structure, 13, 919-928.
-
(2005)
Structure
, vol.13
, pp. 919-928
-
-
Coles, M.1
Djuranovic, S.2
Söding, J.3
Frickey, T.4
Koretke, K.5
Truffault, V.6
Martin, J.7
Lupas, A.N.8
-
27
-
-
17744372267
-
The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases
-
Pei,J. and Grishin,N.V. (2005) The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases. Protein Sci., 14, 1370-1374.
-
(2005)
Protein Sci.
, vol.14
, pp. 1370-1374
-
-
Pei, J.1
Grishin, N.V.2
-
28
-
-
10044222704
-
CLANS: A Java application for visualizing protein families based on pairwise similarity
-
Frickey,T. and Lupas,A. (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics, 20, 3702-3704.
-
(2004)
Bioinformatics
, vol.20
, pp. 3702-3704
-
-
Frickey, T.1
Lupas, A.2
-
29
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Söding,J., Biegert,A. and Lupas,A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Söding, J.1
Biegert, A.2
Lupas, A.N.3
-
30
-
-
1342288004
-
The Jalview Java alignment editor
-
Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.
-
(2004)
Bioinformatics
, vol.20
, pp. 426-427
-
-
Clamp, M.1
Cuff, J.2
Searle, S.M.3
Barton, G.J.4
|