-
1
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
2
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C, Hughey R, (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
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (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
-
4
-
-
27844519262
-
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins
-
Sandhya S, Chakrabarti S, Abhinandan KR, Sowdhamini R, 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
-
5
-
-
0027994453
-
Recognition of related proteins by iterative template refinement (ITR)
-
Yi TM, Lander ES, (1994) Recognition of related proteins by iterative template refinement (ITR). Protein Sci 3: 1315-1328.
-
(1994)
Protein Sci
, vol.3
, pp. 1315-1328
-
-
Yi, T.M.1
Lander, E.S.2
-
6
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park J, Teichmann SA, Hubbard T, Chothia C, (1997) Intermediate sequences increase the detection of homology between sequences. Journal of Molecular Biology 273: 349-354.
-
(1997)
Journal of Molecular Biology
, vol.273
, pp. 349-354
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
7
-
-
0032940341
-
Combining sensitive database searches with multiple intermediates to detect distant homologues
-
Salamov AA, Suwa M, Orengo CA, Swindells MB, (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng 12: 95-100.
-
(1999)
Protein Eng
, vol.12
, pp. 95-100
-
-
Salamov, A.A.1
Suwa, M.2
Orengo, C.A.3
Swindells, M.B.4
-
8
-
-
0034491129
-
Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
-
Li W, Pio F, Pawłowski K, 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
Pawłowski, K.3
Godzik, A.4
-
9
-
-
33846947543
-
Motif kernel generated by genetic programming improves remote homology and fold detection
-
Handstad T, Hestnes A, Saetrom P, (2007) Motif kernel generated by genetic programming improves remote homology and fold detection. BMC Bioinformatics 8: 23.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 23
-
-
Handstad, T.1
Hestnes, A.2
Saetrom, P.3
-
10
-
-
4944225083
-
Remote homology detection: a motif based approach
-
Ben-Hur A, (2003) Remote homology detection: a motif based approach. Bioinformatics 19: 26i-33.
-
(2003)
Bioinformatics
, vol.19
-
-
Ben-Hur, A.1
-
11
-
-
0034518144
-
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases
-
Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM, (2000) Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinformatics 16: 988-1002.
-
(2000)
Bioinformatics
, vol.16
, pp. 988-1002
-
-
Wallqvist, A.1
Fukunishi, Y.2
Murphy, L.R.3
Fadel, A.4
Levy, R.M.5
-
12
-
-
33745616114
-
A machine learning information retrieval approach to protein fold recognition
-
Cheng J, Baldi P, (2006) A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22: 1456-1463.
-
(2006)
Bioinformatics
, vol.22
, pp. 1456-1463
-
-
Cheng, J.1
Baldi, P.2
-
13
-
-
30344449457
-
Assessment of fold recognition predictions in CASP6
-
Wang G, Jin Y, Dunbrack RL, (2005) Assessment of fold recognition predictions in CASP6. Proteins 61Suppl 7: 46-66.
-
(2005)
Proteins
, vol.61
, pp. 46-66
-
-
Wang, G.1
Jin, Y.2
Dunbrack, R.L.3
-
14
-
-
34250674964
-
The WWWH of remote homolog detection: The state of the art
-
Fariselli P, Rossi I, Capriotti E, Casadio R, (2007) The WWWH of remote homolog detection: The state of the art. Briefings in Bioinformatics 8: 78-87.
-
(2007)
Briefings in Bioinformatics
, vol.8
, pp. 78-87
-
-
Fariselli, P.1
Rossi, I.2
Capriotti, E.3
Casadio, R.4
-
15
-
-
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
-
16
-
-
0034062874
-
Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL
-
Teichmann SA, Chothia C, Church GM, Park J, (2000) Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL. Bioinformatics 16: 117-124.
-
(2000)
Bioinformatics
, vol.16
, pp. 117-124
-
-
Teichmann, S.A.1
Chothia, C.2
Church, G.M.3
Park, J.4
-
17
-
-
11844252119
-
A cut above the rest: the regulatory function of plant proteases
-
Schaller A, (2004) A cut above the rest: the regulatory function of plant proteases. Planta 220: 183-197.
-
(2004)
Planta
, vol.220
, pp. 183-197
-
-
Schaller, A.1
-
18
-
-
0036776905
-
Cutting edge of chloroplast proteolysis
-
Adam Z, Clarke AK, (2002) Cutting edge of chloroplast proteolysis. Trends Plant Sci 7: 451-456.
-
(2002)
Trends Plant Sci
, vol.7
, pp. 451-456
-
-
Adam, Z.1
Clarke, A.K.2
-
19
-
-
0035027728
-
Chloroplast and Mitochondrial Proteases in Arabidopsis. A Proposed Nomenclature
-
Adam Z, Adamska I, Nakabayashi K, Ostersetzer O, Haussuhl K, et al. (2001) Chloroplast and Mitochondrial Proteases in Arabidopsis. A Proposed Nomenclature. Plant Physiology 125: 1912-1918.
-
(2001)
Plant Physiology
, vol.125
, pp. 1912-1918
-
-
Adam, Z.1
Adamska, I.2
Nakabayashi, K.3
Ostersetzer, O.4
Haussuhl, K.5
-
20
-
-
0036618905
-
Plant proteases, protein degradation, and oxidative stress: role of peroxisomes
-
Palma JM, Sandalio LM, Javier Corpas F, Romero-Puertas MC, McCarthy I, et al. (2002) Plant proteases, protein degradation, and oxidative stress: role of peroxisomes. Plant Physiology and Biochemistry 40: 521-530.
-
(2002)
Plant Physiology and Biochemistry
, vol.40
, pp. 521-530
-
-
Palma, J.M.1
Sandalio, L.M.2
Javier Corpas, F.3
Romero-Puertas, M.C.4
McCarthy, I.5
-
21
-
-
33748630199
-
Cross genome comparisons of serine proteases in Arabidopsis and rice
-
Tripathi L, Sowdhamini R, (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics 7: 200.
-
(2006)
BMC Genomics
, vol.7
, pp. 200
-
-
Tripathi, L.1
Sowdhamini, R.2
-
22
-
-
0036178438
-
The prolyl oligopeptidase family
-
Polgár L, (2002) The prolyl oligopeptidase family. Cell Mol Life Sci 59: 349-362.
-
(2002)
Cell Mol Life Sci
, vol.59
, pp. 349-362
-
-
Polgár, L.1
-
23
-
-
0043073112
-
Prolyl peptidases: a serine protease subfamily with high potential for drug discovery
-
Rosenblum JS, Kozarich JW, (2003) Prolyl peptidases: a serine protease subfamily with high potential for drug discovery. Curr Opin Chem Biol 7: 496-504.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 496-504
-
-
Rosenblum, J.S.1
Kozarich, J.W.2
-
24
-
-
4444266919
-
Rhomboids
-
Freeman M, (2003) Rhomboids. Curr Biol 13: R586.
-
(2003)
Curr Biol
, vol.13
-
-
Freeman, M.1
-
25
-
-
1542374120
-
Proteolysis within the membrane: rhomboids revealed
-
Freeman M, (2004) Proteolysis within the membrane: rhomboids revealed. Nat Rev Mol Cell Biol 5: 188-197.
-
(2004)
Nat Rev Mol Cell Biol
, vol.5
, pp. 188-197
-
-
Freeman, M.1
-
26
-
-
14844300797
-
Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases
-
Lemberg MK, Menendez J, Misik A, Garcia M, Koth CM, et al. (2005) Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases. EMBO J 24: 464-472.
-
(2005)
EMBO J
, vol.24
, pp. 464-472
-
-
Lemberg, M.K.1
Menendez, J.2
Misik, A.3
Garcia, M.4
Koth, C.M.5
-
27
-
-
35748974498
-
The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG
-
Wang Y, Maegawa S, Akiyama Y, Ha Y, (2007) The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J Mol Biol 374: 1104-1113.
-
(2007)
J Mol Biol
, vol.374
, pp. 1104-1113
-
-
Wang, Y.1
Maegawa, S.2
Akiyama, Y.3
Ha, Y.4
-
28
-
-
0023643147
-
The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry
-
Bode W, Papamokos E, Musil D, (1987) The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry. Eur J Biochem 166: 673-692.
-
(1987)
Eur J Biochem
, vol.166
, pp. 673-692
-
-
Bode, W.1
Papamokos, E.2
Musil, D.3
-
29
-
-
55449107813
-
Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family
-
Rautengarten C, Steinhauser D, Büssis D, Stintzi A, Schaller A, et al. (2005) Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family. PLoS Comput Biol 1: e40.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Rautengarten, C.1
Steinhauser, D.2
Büssis, D.3
Stintzi, A.4
Schaller, A.5
-
30
-
-
70350133848
-
Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase 3
-
Ottmann C, Rose R, Huttenlocher F, Cedzich A, Hauske P, et al. (2009) Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase 3. Proc Natl Acad Sci USA 106: 17223-17228.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17223-17228
-
-
Ottmann, C.1
Rose, R.2
Huttenlocher, F.3
Cedzich, A.4
Hauske, P.5
-
31
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247: 536-540.
-
(1995)
Journal of Molecular Biology
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
32
-
-
0037246028
-
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
-
Gowri VS, Pandit SB, Karthik PS, Srinivasan N, Balaji S, (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Research 31: 486-488.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 486-488
-
-
Gowri, V.S.1
Pandit, S.B.2
Karthik, P.S.3
Srinivasan, N.4
Balaji, S.5
-
33
-
-
84874254733
-
-
Accessed 2008 August 10
-
(2008) TAIR website. Available: http://www.arabidopsis.org/Accessed 2008 August 10.
-
(2008)
TAIR website
-
-
-
34
-
-
33846101405
-
The TIGR Rice Genome Annotation Resource: improvements and new features
-
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Ouyang, S.1
Zhu, W.2
Hamilton, J.3
Lin, H.4
Campbell, M.5
-
35
-
-
33846033400
-
CDD: a conserved domain database for interactive domain family analysis
-
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, et al. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research 35: D237-D240.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Marchler-Bauer, A.1
Anderson, J.B.2
Derbyshire, M.K.3
DeWeese-Scott, C.4
Gonzales, N.R.5
-
37
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: an overview
-
Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.F.4
Nielsen, H.5
-
38
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnády GE, Simon I, (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850.
-
(2001)
Bioinformatics
, vol.17
, pp. 849-850
-
-
Tusnády, G.E.1
Simon, I.2
-
39
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, (2004) The Pfam protein families database. Nucleic Acids Research 32: 138D-141.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 138-1141
-
-
Bateman, A.1
-
40
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
41
-
-
34248574685
-
Strategies for the effective identification of remotely related sequences in multiple PSSM search approach
-
Gowri VS, Tina KG, Krishnadev O, Srinivasan N, (2007) Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. Proteins 67: 789-794.
-
(2007)
Proteins
, vol.67
, pp. 789-794
-
-
Gowri, V.S.1
Tina, K.G.2
Krishnadev, O.3
Srinivasan, N.4
-
42
-
-
16244423379
-
Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions
-
Ekman D, Björklund AK, Frey-Skött J, Elofsson A, (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol 348: 231-243.
-
(2005)
J Mol Biol
, vol.348
, pp. 231-243
-
-
Ekman, D.1
Björklund, A.K.2
Frey-Skött, J.3
Elofsson, A.4
-
43
-
-
0034887573
-
Scale-free behavior in protein domain networks
-
Wuchty S, (2001) Scale-free behavior in protein domain networks. Mol Biol Evol 18: 1694-1702.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1694-1702
-
-
Wuchty, S.1
-
44
-
-
0242323637
-
Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination
-
Apic G, Huber W, Teichmann SA, (2003) Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics 4: 67-78.
-
(2003)
J Struct Funct Genomics
, vol.4
, pp. 67-78
-
-
Apic, G.1
Huber, W.2
Teichmann, S.A.3
-
46
-
-
67649811284
-
The protease-associated domain and C-terminal extension are required for zymogen processing, sorting within the secretory pathway, and activity of tomato subtilase 3 (SlSBT3)
-
Cedzich A, Huttenlocher F, Kuhn BM, Pfannstiel J, Gabler L, et al. (2009) The protease-associated domain and C-terminal extension are required for zymogen processing, sorting within the secretory pathway, and activity of tomato subtilase 3 (SlSBT3). J Biol Chem 284: 14068-14078.
-
(2009)
J Biol Chem
, vol.284
, pp. 14068-14078
-
-
Cedzich, A.1
Huttenlocher, F.2
Kuhn, B.M.3
Pfannstiel, J.4
Gabler, L.5
-
47
-
-
0033769531
-
The PA domain: A protease-associated domain
-
Mahon P, Bateman A, (2000) The PA domain: A protease-associated domain. Protein Science 9: 1930-1934.
-
(2000)
Protein Science
, vol.9
, pp. 1930-1934
-
-
Mahon, P.1
Bateman, A.2
-
48
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park J, Teichmann SA, Hubbard T, 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
|