-
1
-
-
0030464952
-
Detection of non-topological motifs in protein structures
-
Alesker,V. et al. (1996) Detection of non-topological motifs in protein structures. Protein Eng., 9, 1103-1119.
-
(1996)
Protein Eng
, vol.9
, pp. 1103-1119
-
-
Alesker, V.1
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S. 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.1
-
3
-
-
0043159108
-
Elongation factors in protein biosynthesis
-
Andersen,G.R. et al. (2003) Elongation factors in protein biosynthesis. Trends Biochem. Sci., 28, 434-441.
-
(2003)
Trends Biochem. Sci
, vol.28
, pp. 434-441
-
-
Andersen, G.R.1
-
4
-
-
2442645157
-
Rapid 3D protein structure database searching using information retrieval techniques
-
Aung,Z. and Tan,K. (2004) Rapid 3D protein structure database searching using information retrieval techniques. Bioinformatics, 20, 1045-1052.
-
(2004)
Bioinformatics
, vol.20
, pp. 1045-1052
-
-
Aung, Z.1
Tan, K.2
-
5
-
-
34248185418
-
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
-
Ausiello,G. et al. (2007) Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics, 8 (Suppl. 1), S24.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 1
-
-
Ausiello, G.1
-
6
-
-
2442701936
-
Progress: Simultaneous searching of protein databases by sequence and structure
-
Bhattacharya,A. et al. (2004) Progress: Simultaneous searching of protein databases by sequence and structure. Pac. Symp. Biocomput. 9, 264-275.
-
(2004)
Pac. Symp. Biocomput
, vol.9
, pp. 264-275
-
-
Bhattacharya, A.1
-
7
-
-
33846704538
-
Vorolign: Fast structural alignment using Voronoi contacts
-
Birzele,F. et al. (2007) Vorolign: Fast structural alignment using Voronoi contacts. Bioinformatics, 23, e205-e211.
-
(2007)
Bioinformatics
, vol.23
-
-
Birzele, F.1
-
8
-
-
33745027619
-
A gold standard set of mechanistically diverse enzyme superfamilies
-
Brown,S. et al. (2006) A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol., 7, R8.
-
(2006)
Genome Biol
, vol.7
-
-
Brown, S.1
-
9
-
-
24344476038
-
Yakusa: A fast structural database scanning method
-
Carpentier,M. et al. (2005) Yakusa: A fast structural database scanning method. Proteins, 61, 137-151.
-
(2005)
Proteins
, vol.61
, pp. 137-151
-
-
Carpentier, M.1
-
10
-
-
0348129526
-
The ASTRAL compendium in 2004
-
Chandonia,J. et al. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, 189-192.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 189-192
-
-
Chandonia, J.1
-
11
-
-
0034855724
-
Amino acid similarity matrices based on force fields
-
Dosztanyi,Z. and Torda,A. (2001) Amino acid similarity matrices based on force fields. Bioinformatics, 17, 686-699.
-
(2001)
Bioinformatics
, vol.17
, pp. 686-699
-
-
Dosztanyi, Z.1
Torda, A.2
-
12
-
-
0030310317
-
Assessing the performance of fold recognition methods by means of a comprehensive benchmark
-
World Scientific Publishing, Hawaii, pp
-
Fischer,D. et al. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac. Symp. Biocomput., World Scientific Publishing, Hawaii, pp. 300-318.
-
(1996)
Pac. Symp. Biocomput
, pp. 300-318
-
-
Fischer, D.1
-
13
-
-
13844292778
-
The SSEA server for protein secondary structure alignment
-
Fontana,P. et al. (2005) The SSEA server for protein secondary structure alignment. Bioinformatics, 21, 393-395.
-
(2005)
Bioinformatics
, vol.21
, pp. 393-395
-
-
Fontana, P.1
-
14
-
-
23444459516
-
Connecting the protein structure universe by using sparse recurring fragments
-
Friedberg,I. and Godzik,A. (2005) Connecting the protein structure universe by using sparse recurring fragments. Structure, 13, 1213-1224.
-
(2005)
Structure
, vol.13
, pp. 1213-1224
-
-
Friedberg, I.1
Godzik, A.2
-
15
-
-
0035342441
-
Lattice protein folding with two and four-body statistical potentials
-
Gan,H. et al. (2001) Lattice protein folding with two and four-body statistical potentials. Proteins, 43, 161-174.
-
(2001)
Proteins
, vol.43
, pp. 161-174
-
-
Gan, H.1
-
16
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
-
(1993)
J. Mol. Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
17
-
-
3042533397
-
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
-
Ilyin,V.A. et al. (2004) Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci., 13, 1865-1874.
-
(2004)
Protein Sci
, vol.13
, pp. 1865-1874
-
-
Ilyin, V.A.1
-
18
-
-
0034842485
-
Circularly permuted proteins in the protein structure database
-
Jung,J. and Lee,B. (2001) Circularly permuted proteins in the protein structure database. Protein Sci., 10, 1881-1886.
-
(2001)
Protein Sci
, vol.10
, pp. 1881-1886
-
-
Jung, J.1
Lee, B.2
-
19
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
Kabsch,W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr., A34, 827-828.
-
(1978)
Acta Crystallogr
, vol.A34
, pp. 827-828
-
-
Kabsch, W.1
-
20
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
21
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
Kolodny,R. et al. (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol., 346, 1173-1188.
-
(2005)
J. Mol. Biol
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
-
22
-
-
33744805069
-
Protein structure comparison: Implications for the nature of fold space and structure and function prediction
-
Kolodny,R. et al. (2006) Protein structure comparison: implications for the nature of fold space and structure and function prediction. Curr Opin. Struct. Biol., 16, 393-398.
-
(2006)
Curr Opin. Struct. Biol
, vol.16
, pp. 393-398
-
-
Kolodny, R.1
-
23
-
-
17444377949
-
Structural drift: A possible path to protein fold change
-
Krishna,S.S. and Grishin,N.V. (2005) Structural drift: A possible path to protein fold change. Bioinformatics, 21, 1308-1310.
-
(2005)
Bioinformatics
, vol.21
, pp. 1308-1310
-
-
Krishna, S.S.1
Grishin, N.V.2
-
24
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
-
Krishnamoorthy,B. and Tropsha,A. (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics, 18, 1540-1548.
-
(2003)
Bioinformatics
, vol.18
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
25
-
-
0032251894
-
Convergence properties of the nelder-mead simplex method in low dimensions
-
Lagarias,J.C. et al. (1998) Convergence properties of the nelder-mead simplex method in low dimensions. SIAM J. Optim., 9 112-147.
-
(1998)
SIAM J. Optim
, vol.9
, pp. 112-147
-
-
Lagarias, J.C.1
-
26
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
Lathrop,R. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7, 1059-1068.
-
(1994)
Protein Eng
, vol.7
, pp. 1059-1068
-
-
Lathrop, R.1
-
27
-
-
0034458972
-
The ups and downs of protein topology: Rapid comparison of protein structure
-
Martin,A. (2000) The ups and downs of protein topology: Rapid comparison of protein structure. Protein Eng., 13, 829-837.
-
(2000)
Protein Eng
, vol.13
, pp. 829-837
-
-
Martin, A.1
-
28
-
-
0034678924
-
Structure of the fMet-tRNAfMet-binding domain of B.stearothermophilus initiation factor IF2
-
Meunier,S. et al. (2000) Structure of the fMet-tRNAfMet-binding domain of B.stearothermophilus initiation factor IF2. EMBO J., 19, 1918-1926.
-
(2000)
EMBO J
, vol.19
, pp. 1918-1926
-
-
Meunier, S.1
-
29
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
-
30
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol Biol., 48, 443.
-
(1970)
J. Mol Biol
, vol.48
, pp. 443
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
31
-
-
0030777303
-
CATH: A hierarchic classification of protein domain structures
-
Orengo,C. et al. (1997) CATH: A hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.1
-
32
-
-
0036839162
-
Mammoth (matching molecular models obtained from theory): An automated method for model comparison
-
Ortiz,A. et al. (2002) Mammoth (matching molecular models obtained from theory): An automated method for model comparison. Protein Sci. 11, 2606-2621.
-
(2002)
Protein Sci
, vol.11
, pp. 2606-2621
-
-
Ortiz, A.1
-
33
-
-
0015977588
-
The interpretation of protein structures: Total volume, group volume distributions and packing density
-
Richards,F. (1974) The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.
-
(1974)
J. Mol. Biol
, vol.82
, pp. 1-14
-
-
Richards, F.1
-
34
-
-
19544385241
-
Structure alignment via Delaunay tetrahedralization
-
Roach,J. et al. (2005) Structure alignment via Delaunay tetrahedralization. Proteins, 60, 66-81.
-
(2005)
Proteins
, vol.60
, pp. 66-81
-
-
Roach, J.1
-
35
-
-
44249087376
-
Amino acid substitution matrices based on 4-body Delaunay contact profiles
-
Boston, MA, USA, pp
-
Sacan,A. and Toroslu,I.H. (2007) Amino acid substitution matrices based on 4-body Delaunay contact profiles. In IEEE Trans. of the 7th International Symposium on Bioinformatics and Bioengineering (IEEE-BIBE2007). Boston, MA, USA, pp. 796-802.
-
(2007)
IEEE Trans. of the 7th International Symposium on Bioinformatics and Bioengineering (IEEE-BIBE2007)
, pp. 796-802
-
-
Sacan, A.1
Toroslu, I.H.2
-
36
-
-
34147112346
-
LFM-pro: A tool for detecting significant local structural sites in proteins
-
Sacan,A. et al. (2007) LFM-pro: A tool for detecting significant local structural sites in proteins. Bioinformatics, 23, 709-716.
-
(2007)
Bioinformatics
, vol.23
, pp. 709-716
-
-
Sacan, A.1
-
37
-
-
0000821965
-
On the theory and computation of evolutionary distances
-
Sellers,P. (1974) On the theory and computation of evolutionary distances. J. Appl. Math., 26, 787-793.
-
(1974)
J. Appl. Math
, vol.26
, pp. 787-793
-
-
Sellers, P.1
-
38
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov,I. and Bourne,P. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng, 11, 739-747.
-
(1998)
Protein Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.1
Bourne, P.2
-
39
-
-
5444273023
-
Improvements in distance-based indexing
-
Washington, DC, USA, pp
-
Taskin,M. and Ozsoyoglu,Z.M. (2004) Improvements in distance-based indexing. In IEEE Proceedings of the 16th International Conference on Science and Statistic. Database Management. Washington, DC, USA, pp. 161-170.
-
(2004)
IEEE Proceedings of the 16th International Conference on Science and Statistic. Database Management
, pp. 161-170
-
-
Taskin, M.1
Ozsoyoglu, Z.M.2
-
41
-
-
34250167965
-
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
-
Tung,C.-H. et al. (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol., 8, R31.1-R31.16.
-
(2007)
Genome Biol
, vol.8
-
-
Tung, C.-H.1
-
42
-
-
0034518144
-
Iterative sequence/secondary structure search for protein homologs
-
Wallqvist,A. et al. (2000) Iterative sequence/secondary structure search for protein homologs. Bioinformatics, 16, 988-1002.
-
(2000)
Bioinformatics
, vol.16
, pp. 988-1002
-
-
Wallqvist, A.1
-
43
-
-
10744233704
-
Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum
-
Wu,B. et al. (2003) Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum. Protein Sci., 12, 2831-2837.
-
(2003)
Protein Sci
, vol.12
, pp. 2831-2837
-
-
Wu, B.1
-
44
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
45
-
-
0032785381
-
A comparison of amino acid distance measures using procrustes analysis
-
Zintzaras,E. (1999) A comparison of amino acid distance measures using procrustes analysis. Comput. Biol. Med., 29, 283-288.
-
(1999)
Comput. Biol. Med
, vol.29
, pp. 283-288
-
-
Zintzaras, E.1
|