-
1
-
-
0015859467
-
Principles that govern the folding of polypeptide chains
-
Anfinsen C.B. Principles that govern the folding of polypeptide chains. Science 181 (1973) 223-230
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0242355016
-
Structure-based functional inference in structural genomics
-
Kim S.H., Shin D.H., Choi I.G., Schulze-Gahmen U., Chen S., and Kim R. Structure-based functional inference in structural genomics. J Struct Funct Genomics 4 (2003) 129-135
-
(2003)
J Struct Funct Genomics
, vol.4
, pp. 129-135
-
-
Kim, S.H.1
Shin, D.H.2
Choi, I.G.3
Schulze-Gahmen, U.4
Chen, S.5
Kim, R.6
-
3
-
-
0027404023
-
Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases
-
Bork P., Sander C., and Valencia A. Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Protein Sci 2 (1993) 31-40
-
(1993)
Protein Sci
, vol.2
, pp. 31-40
-
-
Bork, P.1
Sander, C.2
Valencia, A.3
-
4
-
-
0032568859
-
Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
-
Russell R.B. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 279 (1998) 1211-1227
-
(1998)
J Mol Biol
, vol.279
, pp. 1211-1227
-
-
Russell, R.B.1
-
5
-
-
0035106757
-
Sialidase-like Asp-boxes: sequence-similar structures within different protein folds
-
Copley R.R., Russell R.B., and Ponting C.P. Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. Protein Sci 10 (2001) 285-292
-
(2001)
Protein Sci
, vol.10
, pp. 285-292
-
-
Copley, R.R.1
Russell, R.B.2
Ponting, C.P.3
-
6
-
-
34248185418
-
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
-
Ausiello G., Peluso D., Via A., and Helmer-Citterich M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics 8 Suppl. 1 (2007) S24
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 1
-
-
Ausiello, G.1
Peluso, D.2
Via, A.3
Helmer-Citterich, M.4
-
8
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C., and Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J 5 (1986) 823-826
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
9
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
10
-
-
0030777303
-
CATH: a hierarchic classification of protein domain structures
-
Orengo C.A., Michie A.D., Jones D.T., Swindells M.B., and Thornton J.M. CATH: a hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1110
-
(1997)
Structure
, vol.5
, pp. 1093-1110
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, D.T.3
Swindells, M.B.4
Thornton, J.M.5
-
12
-
-
0029881326
-
Towards meeting the Paracelsus challenge: the design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein
-
Jones D.T., Moody C.M., Uppenbink J., Viles J.H., Doyle P.M., Harris C.J., Pearl L.H., Sadler P.J., and Thornton J.M. Towards meeting the Paracelsus challenge: the design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein. Proteins 24 (1995) 502-513
-
(1995)
Proteins
, vol.24
, pp. 502-513
-
-
Jones, D.T.1
Moody, C.M.2
Uppenbink, J.3
Viles, J.H.4
Doyle, P.M.5
Harris, C.J.6
Pearl, L.H.7
Sadler, P.J.8
Thornton, J.M.9
-
13
-
-
0031181666
-
Protein folding and the Paracelsus challenge
-
Rose G.D. Protein folding and the Paracelsus challenge. Nat Struct Biol 4 (1997) 512-514
-
(1997)
Nat Struct Biol
, vol.4
, pp. 512-514
-
-
Rose, G.D.1
-
14
-
-
0030986375
-
Protein alchemy: changing beta-sheet into alpha-helix
-
Dalal S., Balasubramanian S., and Regan L. Protein alchemy: changing beta-sheet into alpha-helix. Nat Struct Biol 4 (1997) 548-552
-
(1997)
Nat Struct Biol
, vol.4
, pp. 548-552
-
-
Dalal, S.1
Balasubramanian, S.2
Regan, L.3
-
15
-
-
0032006183
-
A hybrid sequence approach to the paracelsus challenge
-
Shao-Min Y., and Clarke N.D. A hybrid sequence approach to the paracelsus challenge. Proteins 30 (1998) 136-143
-
(1998)
Proteins
, vol.30
, pp. 136-143
-
-
Shao-Min, Y.1
Clarke, N.D.2
-
16
-
-
34547499110
-
The design and characterization of two proteins with 88% sequence identity but different structure and function
-
Two proteins with 88% sequence identity but markedly different structures are reported.
-
Alexander P.A., He Y., Chen Y., Orban J., and Bryan P.N. The design and characterization of two proteins with 88% sequence identity but different structure and function. PNAS 104 (2007) 11963-11968. Two proteins with 88% sequence identity but markedly different structures are reported.
-
(2007)
PNAS
, vol.104
, pp. 11963-11968
-
-
Alexander, P.A.1
He, Y.2
Chen, Y.3
Orban, J.4
Bryan, P.N.5
-
17
-
-
55749108537
-
NMR structures of two designed proteins with high sequence identity but different fold and function
-
He Y., Chen Y., Alexander P., Bryan P.N., and Orban J. NMR structures of two designed proteins with high sequence identity but different fold and function. PNAS 105 (2008) 14412-14417
-
(2008)
PNAS
, vol.105
, pp. 14412-14417
-
-
He, Y.1
Chen, Y.2
Alexander, P.3
Bryan, P.N.4
Orban J5
-
18
-
-
0033668488
-
An evolutionary bridge to a new protein fold
-
Cordes M.H.J., Burton R.E., Walsh N.P., McKnight C.J., and Sauer R.T. An evolutionary bridge to a new protein fold. Nat Struct Biol 7 (2000) 1129-1132
-
(2000)
Nat Struct Biol
, vol.7
, pp. 1129-1132
-
-
Cordes, M.H.J.1
Burton, R.E.2
Walsh, N.P.3
McKnight, C.J.4
Sauer, R.T.5
-
19
-
-
33748269731
-
Relationship between sequence determinants of stability for two natural homologous proteins with different folds
-
Mutagenesis experiments are used to determine a possible intermediate sequence between two Cro proteins.
-
Van Dorn L.O., Newlove T., Chang S., Ingram W.M., and Cordes M.H. Relationship between sequence determinants of stability for two natural homologous proteins with different folds. Biochemistry 45 (2006) 10542-10553. Mutagenesis experiments are used to determine a possible intermediate sequence between two Cro proteins.
-
(2006)
Biochemistry
, vol.45
, pp. 10542-10553
-
-
Van Dorn, L.O.1
Newlove, T.2
Chang, S.3
Ingram, W.M.4
Cordes, M.H.5
-
20
-
-
33846209932
-
Continuous molecular evolution of protein-domain structures by single amino acid changes
-
A G to P point mutation is shown to cause a small, cysteine-rich protein of cnidarian nematocyst collagen to adopt two ground-state structures with different disulfide-bonding patterns and a grossly changed overall conformation.
-
Meier S., Jensen P.R., David C.N., Chapman J., Holstein T.W., Grzesieck S., and Ozbeck S. Continuous molecular evolution of protein-domain structures by single amino acid changes. Curr Biol 17 (2007) 173-178. A G to P point mutation is shown to cause a small, cysteine-rich protein of cnidarian nematocyst collagen to adopt two ground-state structures with different disulfide-bonding patterns and a grossly changed overall conformation.
-
(2007)
Curr Biol
, vol.17
, pp. 173-178
-
-
Meier, S.1
Jensen, P.R.2
David, C.N.3
Chapman, J.4
Holstein, T.W.5
Grzesieck, S.6
Ozbeck, S.7
-
21
-
-
33751091763
-
Cognate ligand domain mapping for enzymes
-
Bashton M., Nobeli I., and Thornton J.M. Cognate ligand domain mapping for enzymes. J Mol Biol 364 (2006) 836-852
-
(2006)
J Mol Biol
, vol.364
, pp. 836-852
-
-
Bashton, M.1
Nobeli, I.2
Thornton, J.M.3
-
22
-
-
38549161051
-
PROCOGNATE: A cognate ligand domain mapping for enzymes
-
Bashton M., Nobeli I., and Thornton J.M. PROCOGNATE: A cognate ligand domain mapping for enzymes. Nucleic Acids Res 36 (2008) D618-D622
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Bashton, M.1
Nobeli, I.2
Thornton, J.M.3
-
23
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 372 (2007) 774-797
-
(2007)
J Mol Biol
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
24
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The gene ontology consortium
-
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25 (2000) 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
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
26
-
-
30344440806
-
The prediction of protein function at CASP 6
-
Soro S., and Tramontano A. The prediction of protein function at CASP 6. Proteins 61 S7 (2005) 201-213
-
(2005)
Proteins
, vol.61
, Issue.SUPPL.7
, pp. 201-213
-
-
Soro, S.1
Tramontano, A.2
-
27
-
-
33745190979
-
Revisiting the prediction of protein function at CASP 6
-
A follow-up of the CASP function prediction exercise once experimental validations were available for ten of the targets. Some evidence that the consensus of methods, as used in the original assessment, was usually correct is provided but the assessment remains difficult even once experimental results are available.
-
Pellegrini-Calace M., Soro S., and Tramontano A. Revisiting the prediction of protein function at CASP 6. FEBS J 273 (2006) 2977-2983. A follow-up of the CASP function prediction exercise once experimental validations were available for ten of the targets. Some evidence that the consensus of methods, as used in the original assessment, was usually correct is provided but the assessment remains difficult even once experimental results are available.
-
(2006)
FEBS J
, vol.273
, pp. 2977-2983
-
-
Pellegrini-Calace, M.1
Soro, S.2
Tramontano, A.3
-
28
-
-
34547421112
-
Defining functional distance using manifold embeddings of gene ontology annotations
-
Lerman G., and Shakhnovich B.E. Defining functional distance using manifold embeddings of gene ontology annotations. Proc Natl Acad Sci U S A 104 (2007) 11334-11339
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 11334-11339
-
-
Lerman, G.1
Shakhnovich, B.E.2
-
29
-
-
56649124843
-
The protein feature ontology: a tool for the unification of protein feature annotations
-
Reeves G.A., Eilbeck K., Magrane M., O'Donovan C., Montecchi-Palazzi L., Harris M.A., Orchard S., Jimenez R.C., Prlic A., Hubbard T.J., et al. The protein feature ontology: a tool for the unification of protein feature annotations. Bioinformatics 24 (2008) 2767-2772
-
(2008)
Bioinformatics
, vol.24
, pp. 2767-2772
-
-
Reeves, G.A.1
Eilbeck, K.2
Magrane, M.3
O'Donovan, C.4
Montecchi-Palazzi, L.5
Harris, M.A.6
Orchard, S.7
Jimenez, R.C.8
Prlic, A.9
Hubbard, T.J.10
-
30
-
-
48249136122
-
Integrating biological data-the distributed annotation system
-
Jenkinson A.M., Albrecht M., Birney E., Blankenburg H., Down T., Finn R.D., Hermjakob H., Hubbard T.J., Jimenez R.C., Jones P., et al. Integrating biological data-the distributed annotation system. BMC Bioinformatics 9 Suppl. 8 (2008) S3
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 8
-
-
Jenkinson, A.M.1
Albrecht, M.2
Birney, E.3
Blankenburg, H.4
Down, T.5
Finn, R.D.6
Hermjakob, H.7
Hubbard, T.J.8
Jimenez, R.C.9
Jones, P.10
-
31
-
-
58149161724
-
Genome and proteome annotation: organization, interpretation and integration
-
Reeves G.A., Talavera D., and Thornton J.M. Genome and proteome annotation: organization, interpretation and integration. J R Soc Interface 6 (2009) 129-147
-
(2009)
J R Soc Interface
, vol.6
, pp. 129-147
-
-
Reeves, G.A.1
Talavera, D.2
Thornton, J.M.3
-
32
-
-
0038169950
-
Ligand binding: functional site location, similarity and docking
-
Campbell S.J., Gold N.D., Jackson R.M., and Westhead D.R. Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol 13 (2003) 389-395
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 389-395
-
-
Campbell, S.J.1
Gold, N.D.2
Jackson, R.M.3
Westhead, D.R.4
-
33
-
-
14744305761
-
Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families
-
Torrance J.W., Bartlett G.J., Porter C.T., and Thornton J.M. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 347 (2005) 565-581
-
(2005)
J Mol Biol
, vol.347
, pp. 565-581
-
-
Torrance, J.W.1
Bartlett, G.J.2
Porter, C.T.3
Thornton, J.M.4
-
34
-
-
4143055915
-
Predicting metal-binding site residues in low-resolution structural models
-
Sodhi J.S., Bryson K., McGuffin L.J., Ward J.J., Wernisch L., and Jones D.T. Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 342 (2004) 307-320
-
(2004)
J Mol Biol
, vol.342
, pp. 307-320
-
-
Sodhi, J.S.1
Bryson, K.2
McGuffin, L.J.3
Ward, J.J.4
Wernisch, L.5
Jones, D.T.6
-
35
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent 'profile-profile alignments'
-
Xie L., and Bourne P.E. Detecting evolutionary relationships across existing fold space, using sequence order-independent 'profile-profile alignments'. PNAS 105 (2008) 5441-5446
-
(2008)
PNAS
, vol.105
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
36
-
-
6944227836
-
Automated prediction of protein function and detection of functional sites from structure
-
Pazos F., and Sternberg M.J.E. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A 101 (2004) 14754-14759
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 14754-14759
-
-
Pazos, F.1
Sternberg, M.J.E.2
-
37
-
-
27144551715
-
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
-
Cheng G., Qian B., Samudrala R., and Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res 33 (2005) 5861-5867
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5861-5867
-
-
Cheng, G.1
Qian, B.2
Samudrala, R.3
Baker, D.4
-
38
-
-
37449004656
-
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases
-
Favia A.D., Nobeli I., Glaser F., and Thornton J.M. Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol 375 (2008) 855-874
-
(2008)
J Mol Biol
, vol.375
, pp. 855-874
-
-
Favia, A.D.1
Nobeli, I.2
Glaser, F.3
Thornton, J.M.4
-
39
-
-
33646254603
-
A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships
-
Gold N.D., and Jackson R.M. A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J Chem Inf Model 46 (2006) 736-742
-
(2006)
J Chem Inf Model
, vol.46
, pp. 736-742
-
-
Gold, N.D.1
Jackson, R.M.2
-
40
-
-
36448948641
-
The Poisson Index: a new probabilistic model for protein-ligand binding site similarity
-
Davies J.R., Jackson R.M., Mardia K.V., and Taylor C.C. The Poisson Index: a new probabilistic model for protein-ligand binding site similarity. Bioinformatics 23 (2008) 3001-3008
-
(2008)
Bioinformatics
, vol.23
, pp. 3001-3008
-
-
Davies, J.R.1
Jackson, R.M.2
Mardia, K.V.3
Taylor, C.C.4
-
41
-
-
22544441094
-
ProFunc: a server for predicting protein function from 3D structure
-
Laskowski R.A., Watson J.D., and Thornton J.M. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33 (2005) W89-W93
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Laskowski, R.A.1
Watson, J.D.2
Thornton, J.M.3
-
42
-
-
33947278347
-
Towards fully automated structure-based function prediction in structural genomics: a case study
-
Watson J.D., Sanderson S., Ezersky A., Savchenko A., Edwards A., Orengo C., Joachimiak A., Laskowski R.A., and Thornton J.M. Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol 367 (2007) 1511-1522
-
(2007)
J Mol Biol
, vol.367
, pp. 1511-1522
-
-
Watson, J.D.1
Sanderson, S.2
Ezersky, A.3
Savchenko, A.4
Edwards, A.5
Orengo, C.6
Joachimiak, A.7
Laskowski, R.A.8
Thornton, J.M.9
-
43
-
-
34548432661
-
Piecing together the structure-function puzzle: experiences in the structure-based functional annotation of hypothetical proteins
-
Case studies of seven proteins from E. coli for which successful functional annotations were made using a combination of bioinformatics and experimental techniques.
-
Adams M.A., Suits M.D.L., Zheng J., and Jia Z. Piecing together the structure-function puzzle: experiences in the structure-based functional annotation of hypothetical proteins. Proteomics 7 (2007) 2920-2932. Case studies of seven proteins from E. coli for which successful functional annotations were made using a combination of bioinformatics and experimental techniques.
-
(2007)
Proteomics
, vol.7
, pp. 2920-2932
-
-
Adams, M.A.1
Suits, M.D.L.2
Zheng, J.3
Jia, Z.4
-
44
-
-
31344462177
-
Conformational diversity of ligands bound to proteins
-
Stockwell G.R., and Thornton J.M. Conformational diversity of ligands bound to proteins. JMB 356 (2006) 928-944
-
(2006)
JMB
, vol.356
, pp. 928-944
-
-
Stockwell, G.R.1
Thornton, J.M.2
-
45
-
-
34047273007
-
Functional differentiation of proteins: implications for structural genomics
-
Friedberg I., and Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure 15 (2007) 405-415
-
(2007)
Structure
, vol.15
, pp. 405-415
-
-
Friedberg, I.1
Godzik, A.2
-
46
-
-
0031616362
-
Protein disorder and the evolution of molecular recognition: theory, predictions, and observations
-
Dunker A.K., Garner E., Guilliot S., Romero P., Albrecht K., Hart J., and Obradovic Z. Protein disorder and the evolution of molecular recognition: theory, predictions, and observations. Pacific Symp. Biocomput. 3 (1998) 473-484
-
(1998)
Pacific Symp. Biocomput.
, vol.3
, pp. 473-484
-
-
Dunker, A.K.1
Garner, E.2
Guilliot, S.3
Romero, P.4
Albrecht, K.5
Hart, J.6
Obradovic, Z.7
-
48
-
-
34548448958
-
Inferring function using patterns of native disorder in proteins
-
A fully automated method is presented for predicting the function of proteins, taking into account patterns of predicted disorder within the target protein. Interestingly, disorder features are seen to be one of the most powerful features in determining the correct biological process for a given protein.
-
Lobley A., Swindells M.B., Orengo C.A., and Jones D.T. Inferring function using patterns of native disorder in proteins. PLoS Comput Biol. 3 (2007) e162. A fully automated method is presented for predicting the function of proteins, taking into account patterns of predicted disorder within the target protein. Interestingly, disorder features are seen to be one of the most powerful features in determining the correct biological process for a given protein.
-
(2007)
PLoS Comput Biol.
, vol.3
-
-
Lobley, A.1
Swindells, M.B.2
Orengo, C.A.3
Jones, D.T.4
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