-
1
-
-
0035838976
-
Automated structure based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
Aloy P, Querol E, Aviles F, Sternberg J (2001) Automated structure based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311:395-408
-
(2001)
J Mol Biol
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.3
Sternberg, J.4
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, 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.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
3
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
4
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93-96
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
5
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
0007064893
-
The complete genome sequence of E.coli K-12
-
Blattner F, III GP, Bloch C, Perna N, Burland V, Riley M, Collado-Vides J, Glasner J, Rode C, Mayhew G and others (1997) The complete genome sequence of E.coli K-12. Science 277:1453-1474
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.1
Bloch, C.2
Perna, N.3
Burland, V.4
Riley, M.5
Collado-Vides, J.6
Glasner, J.7
Rode, C.8
Mayhew, G.9
-
7
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016):164-170
-
(1991)
Science
, vol.253
, Issue.5016
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
8
-
-
24944493938
-
Towards high-resolution de novo structure prediction for small proteins
-
Bradley P, Misuara K, Baker D (2005) Towards high-resolution de novo structure prediction for small proteins. Science 309:1868-1871
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misuara, K.2
Baker, D.3
-
9
-
-
0037391107
-
Membrane protein crystallization
-
Caffrey M (2003) Membrane protein crystallization. J Struct Biol 142:108-132
-
(2003)
J Struct Biol
, vol.142
, pp. 108-132
-
-
Caffrey, M.1
-
10
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 12:2001-2014
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.3
-
11
-
-
31144467558
-
The impact of structural genomics: Expectations and outcomes
-
Chandonia J, Brenner S (2006) The impact of structural genomics: expectations and outcomes. Science 311:347-351
-
(2006)
Science
, vol.311
, pp. 347-351
-
-
Chandonia, J.1
Brenner, S.2
-
12
-
-
20144377620
-
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
-
Chen H, Zhou HX (2005a) Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res 33(10):3193-3199
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.10
, pp. 3193-3199
-
-
Chen, H.1
Zhou, H.X.2
-
13
-
-
21744440928
-
Identification and pharmacological characterization of prokineticin 2beta as a selective ligand for prokineticin receptor 1
-
Chen J, Kuei C, Sutton S, Wilson S, Yu J, Kamme F, Mazur C, Lovenberg T, Liu C (2005b) Identification and pharmacological characterization of prokineticin 2beta as a selective ligand for prokineticin receptor 1. Mol Pharmacol 67:2070-2076
-
(2005)
Mol Pharmacol
, vol.67
, pp. 2070-2076
-
-
Chen, J.1
Kuei, C.2
Sutton, S.3
Wilson, S.4
Yu, J.5
Kamme, F.6
Mazur, C.7
Lovenberg, T.8
Liu, C.9
-
14
-
-
84860507958
-
Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
-
Cheng J, Baldi P (2005) Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21(Suppl 1):i75-84
-
(2005)
Bioinformatics
, vol.21
, pp. i75-i84
-
-
Cheng, J.1
Baldi, P.2
-
15
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
Cheng J, Baldi P (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 8:113
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
16
-
-
36448995359
-
High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor
-
Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, others (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318(5854):1258-1265
-
(2007)
Science
, vol.318
, Issue.5854
, pp. 1258-1265
-
-
Cherezov, V.1
Rosenbaum, D.M.2
Hanson, M.A.3
Rasmussen, S.G.4
Thian, F.S.5
Kobilka, T.S.6
Choi, H.J.7
Kuhn, P.8
Weis, W.I.9
Kobilka, B.K.10
-
17
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J (2000) Drug discovery: a historical perspective. Science 287(5460):1960-1964
-
(2000)
Science
, vol.287
, Issue.5460
, pp. 1960-1964
-
-
Drews, J.1
-
18
-
-
0031042157
-
Modeling the G-protein-coupled neuropeptide Y Y1 receptor agonist and antagonist binding sites
-
Du P, Salon JA, Tamm JA, Hou C, Cui W, Walker MW, Adham N, Dhanoa DS, Islam I, Vaysse PJ, others (1997) Modeling the G-protein-coupled neuropeptide Y Y1 receptor agonist and antagonist binding sites. Protein Eng 10:109-117
-
(1997)
Protein Eng
, vol.10
, pp. 109-117
-
-
Du, P.1
Salon, J.A.2
Tamm, J.A.3
Hou, C.4
Cui, W.5
Walker, M.W.6
Adham, N.7
Dhanoa, D.S.8
Islam, I.9
Vaysse, P.J.10
-
19
-
-
0030724017
-
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
-
Fischer D, Eisenberg D (1997) Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci 94:11929-11934
-
(1997)
Proc Natl Acad Sci
, vol.94
, pp. 11929-11934
-
-
Fischer, D.1
Eisenberg, D.2
-
20
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
21
-
-
0032735188
-
Modelling G-protein-coupled receptors for drug design
-
Flower DR (1999) Modelling G-protein-coupled receptors for drug design. Biochim Biophys Acta 1422:207-234
-
(1999)
Biochim Biophys Acta
, vol.1422
, pp. 207-234
-
-
Flower, D.R.1
-
22
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser C, Gocayne J, White O, Adams M, Clayton R, Fleischmann R, Bult C, Kerlavage A, Sutton G, Kelley J, others (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397-403
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.1
Gocayne, J.2
White, O.3
Adams, M.4
Clayton, R.5
Fleischmann, R.6
Bult, C.7
Kerlavage, A.8
Sutton, G.9
Kelley, J.10
-
23
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566-579
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
24
-
-
0037436511
-
Structural genomics: Current progress
-
Gerstein M, Edwards A, Arrowsmith C, Montelione G (2003) Structural genomics: Current progress. Science 299(5613):1663
-
(2003)
Science
, vol.299
, Issue.5613
, pp. 1663
-
-
Gerstein, M.1
Edwards, A.2
Arrowsmith, C.3
Montelione, G.4
-
25
-
-
34250376066
-
Structure and conformational changes in the C-terminal domain of the beta2-adrenoceptor: Insights from fluorescence resonance energy transfer studies
-
Granier S, Kim S, Shafer AM, Ratnala VR, Fung JJ, Zare RN, Kobilka B (2007) Structure and conformational changes in the C-terminal domain of the beta2-adrenoceptor: insights from fluorescence resonance energy transfer studies. J Biol Chem 282:13895-13905
-
(2007)
J Biol Chem
, vol.282
, pp. 13895-13905
-
-
Granier, S.1
Kim, S.2
Shafer, A.M.3
Ratnala, V.R.4
Fung, J.J.5
Zare, R.N.6
Kobilka, B.7
-
27
-
-
0029117219
-
Identification of critical determinants of alpha 1-adrenergic receptor subtype selective agonist binding
-
Hwa J, Graham RM, Perez DM (1995) Identification of critical determinants of alpha 1-adrenergic receptor subtype selective agonist binding. J Biol Chem 270:23189-23195
-
(1995)
J Biol Chem
, vol.270
, pp. 23189-23195
-
-
Hwa, J.1
Graham, R.M.2
Perez, D.M.3
-
28
-
-
56749103466
-
The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist
-
Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, Stevens RC (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322(5905):1211-1217
-
(2008)
Science
, vol.322
, Issue.5905
, pp. 1211-1217
-
-
Jaakola, V.P.1
Griffith, M.T.2
Hanson, M.A.3
Cherezov, V.4
Chien, E.Y.5
Lane, J.R.6
Ijzerman, A.P.7
Stevens, R.C.8
-
29
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones D (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.1
-
30
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358(6381):86-89
-
(1992)
Nature
, vol.358
, Issue.6381
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
31
-
-
0028211273
-
A model recognition approach to the prediction of all-helical membrane protein structure and topology
-
Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33(10):3038-3049
-
(1994)
Biochemistry
, vol.33
, Issue.10
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
32
-
-
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(10):846-856
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
33
-
-
0035964191
-
TOUCHSTONE: An ab initio protein structure prediction method that uses threading based tertiary restraints
-
Kihara D, Lu H, Kolinski A, Skolnick J (2001) TOUCHSTONE: an ab initio protein structure prediction method that uses threading based tertiary restraints Proc Natl Acad Sci 98:10125-10130
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 10125-10130
-
-
Kihara, D.1
Lu, H.2
Kolinski, A.3
Skolnick, J.4
-
34
-
-
0037197857
-
Ab initio protein structure prediction on a genomic scale: Application to Mycoplasma genitalim genome
-
Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J (2002) Ab initio protein structure prediction on a genomic scale: application to Mycoplasma genitalim genome. Proc Natl Acad Sci 99:5993-5998
-
(2002)
Proc Natl Acad Sci
, vol.99
, pp. 5993-5998
-
-
Kihara, D.1
Zhang, Y.2
Lu, H.3
Kolinski, A.4
Skolnick, J.5
-
35
-
-
12944263648
-
Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study
-
Klepeis JL, Wei Y, Hecht MH, Floudas CA (2005) Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 58:560-570
-
(2005)
Proteins
, vol.58
, pp. 560-570
-
-
Klepeis, J.L.1
Wei, Y.2
Hecht, M.H.3
Floudas, C.A.4
-
36
-
-
0033613813
-
Recognition of spatial motifs in protein structures
-
Kleywegt GJ (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285:1887-1897
-
(1999)
J Mol Biol
, vol.285
, pp. 1887-1897
-
-
Kleywegt, G.J.1
-
37
-
-
0028203492
-
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
-
Kolinski A, Skolnick J (1994) Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352
-
(1994)
Proteins
, vol.18
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
38
-
-
36749099341
-
Assessment of CASP7 predictions for template-based modeling targets
-
Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins 69(Suppl 8):38-56
-
(2007)
Proteins
, vol.69
, pp. 38-56
-
-
Kopp, J.1
Bordoli, L.2
Battey, J.N.3
Kiefer, F.4
Schwede, T.5
-
39
-
-
0034704105
-
Coordinated up-regulation by hypoxia of adrenomedullin and one of its putative receptors (RDC-1) in cells of the rat blood-brain barrier
-
Ladoux A, Frelin C (2000) Coordinated up-regulation by hypoxia of adrenomedullin and one of its putative receptors (RDC-1) in cells of the rat blood-brain barrier. J Biol Chem 275:39914-39919
-
(2000)
J Biol Chem
, vol.275
, pp. 39914-39919
-
-
Ladoux, A.1
Frelin, C.2
-
40
-
-
68049138029
-
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks
-
Li Y, Zhang Y (2009) REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 76(3):665-676
-
(2009)
Proteins
, vol.76
, Issue.3
, pp. 665-676
-
-
Li, Y.1
Zhang, Y.2
-
41
-
-
0033545962
-
Protein structure prediction by global optimization of a potential energy function
-
Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA (1999) Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 96(10):5482-5485
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.10
, pp. 5482-5485
-
-
Liwo, A.1
Lee, J.2
Ripoll, D.R.3
Pillardy, J.4
Scheraga, H.A.5
-
42
-
-
36748998785
-
Assessment of predictions submitted for the CASP7 function prediction category
-
Lopez G, Rojas A, Tress M, Valencia A (2007) Assessment of predictions submitted for the CASP7 function prediction category. Proteins 69(Suppl 8):165-174
-
(2007)
Proteins
, vol.69
, pp. 165-174
-
-
Lopez, G.1
Rojas, A.2
Tress, M.3
Valencia, A.4
-
43
-
-
22844448355
-
Structural biology of G protein-coupled receptors
-
Lundstrom K (2005) Structural biology of G protein-coupled receptors. Bioorg Med Chem Lett 15:3654-3657
-
(2005)
Bioorg Med Chem Lett
, vol.15
, pp. 3654-3657
-
-
Lundstrom, K.1
-
44
-
-
38149027753
-
Insight into disulfide bond catalysis in Chlamydia from the structure and function of DsbH, a novel oxidoreductase
-
MacTT, Von Hacht A, Hung KC, Dutton RJ, Boyd D, Bardwell JC, Ulmer TS (2008) Insight into disulfide bond catalysis in Chlamydia from the structure and function of DsbH, a novel oxidoreductase. J Biol Chem 283:824-832
-
(2008)
J Biol Chem
, vol.283
, pp. 824-832
-
-
Mac, T.T.1
Von Hacht, A.2
Hung, K.C.3
Dutton, R.J.4
Boyd, D.5
Bardwell, J.C.6
Ulmer, T.S.7
-
45
-
-
34247362408
-
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
-
Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5:e76
-
(2007)
PLoS Biol
, vol.5
, pp. e76
-
-
Malmstrom, L.1
Riffle, M.2
Strauss, C.E.3
Chivian, D.4
Davis, T.N.5
Bonneau, R.6
Baker, D.7
-
46
-
-
13444262384
-
CDD: A conserved domain database for protein classification
-
Database issue
-
Marchler-Bauer A, Anderson JB, Cherukuri PF, De Weese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, others (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 33 (Database issue):D192-196
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D192-D196
-
-
Marchler-Bauer, A.1
Anderson, J.B.2
Cherukuri, P.F.3
De Weese-Scott, C.4
Geer, L.Y.5
Gwadz, M.6
He, S.7
Hurwitz, D.I.8
Jackson, J.D.9
Ke, Z.10
-
47
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom M, Stuart A, Fiser A, Sanchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Ann Rev Biophys Biomol Struct 29:291-325
-
(2000)
Ann Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.1
Stuart, A.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
48
-
-
0038634975
-
Improvement of GenTHREADER method for genomic fold recognition
-
McGuffin L, Jones D (2003) Improvement of GenTHREADER method for genomic fold recognition. Bioinformatics 19:874-881
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.1
Jones, D.2
-
49
-
-
35648945337
-
CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature
-
Miao Z, Luker KE, Summers BC, Berahovich R, Bhojani MS, Rehemtulla A, Kleer CG, Essner JJ, Nasevicius A, Luker GD, others (2007) CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature. Proc Natl Acad Sci USA 104(40):15735-15740
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.40
, pp. 15735-15740
-
-
Miao, Z.1
Luker, K.E.2
Summers, B.C.3
Berahovich, R.4
Bhojani, M.S.5
Rehemtulla, A.6
Kleer, C.G.7
Essner, J.J.8
Nasevicius, A.9
Luker, G.D.10
-
50
-
-
67349088738
-
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
-
Michino M, Abola E, et al. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 8(6):455-463
-
(2009)
Nat Rev Drug Discov
, vol.8
, Issue.6
, pp. 455-463
-
-
Michino, M.1
Abola, E.2
-
51
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman S, Wunsch C (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443-453
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
52
-
-
21144442648
-
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
-
Oldziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, others (2005) Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci USA 102:7547-7552
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7547-7552
-
-
Oldziej, S.1
Czaplewski, C.2
Liwo, A.3
Chinchio, M.4
Nanias, M.5
Vila, J.A.6
Khalili, M.7
Arnautova, Y.A.8
Jagielska, A.9
Makowski, M.10
-
54
-
-
0034604451
-
Crystal structure of rhodopsin: A G protein-coupled receptor
-
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, others (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289(5480):739-745
-
(2000)
Science
, vol.289
, Issue.5480
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.A.6
Le Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
-
55
-
-
0035038459
-
Regulation of corticotropin-releasing hormone in vitro
-
Pisarska M, Mulchahey JJ, Sheriff S, Geracioti TD, Kasckow JW (2001) Regulation of corticotropin-releasing hormone in vitro. Peptides 22:705-712
-
(2001)
Peptides
, vol.22
, pp. 705-712
-
-
Pisarska, M.1
Mulchahey, J.J.2
Sheriff, S.3
Geracioti, T.D.4
Kasckow, J.W.5
-
56
-
-
36248970132
-
Crystal structure of the human beta2 adrenergic G-protein-coupled receptor
-
Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, others (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450(7168):383-387
-
(2007)
Nature
, vol.450
, Issue.7168
, pp. 383-387
-
-
Rasmussen, S.G.1
Choi, H.J.2
Rosenbaum, D.M.3
Kobilka, T.S.4
Thian, F.S.5
Edwards, P.C.6
Burghammer, M.7
Ratnala, V.R.8
Sanishvili, R.9
Fischetti, R.F.10
-
57
-
-
36749059956
-
Assessment of CASP7 predictions in the high accuracy template-based modeling category
-
Read RJ, Chavali G (2007) Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 69(Suppl 8):27-37
-
(2007)
Proteins
, vol.69
, pp. 27-37
-
-
Read, R.J.1
Chavali, G.2
-
58
-
-
36448978229
-
GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function
-
Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Yao XJ, Weis WI, Stevens RC, others (2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science 318(5854):1266-1273
-
(2007)
Science
, vol.318
, Issue.5854
, pp. 1266-1273
-
-
Rosenbaum, D.M.1
Cherezov, V.2
Hanson, M.A.3
Rasmussen, S.G.4
Thian, F.S.5
Kobilka, T.S.6
Choi, H.J.7
Yao, X.J.8
Weis, W.I.9
Stevens, R.C.10
-
59
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85-94
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
60
-
-
84888679022
-
Large scale benchmarking of protein function prediction using modeled protein structures
-
Submitted
-
Roy A, Kucukural A, Mukherjee S, Hefty PS, Zhang Y (2010) Large scale benchmarking of protein function prediction using modeled protein structures. J Mol Biol (Submitted)
-
(2010)
J Mol Biol
-
-
Roy, A.1
Kucukural, A.2
Mukherjee, S.3
Hefty, P.S.4
Zhang, Y.5
-
61
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell T (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.2
-
62
-
-
0343920731
-
-
Sanchez R, Pieper U, Mirkovic N, Bakker Pd, Wittenstein E, Sali A (2000) MODBASE, a database of annotated comparitive protein structure models Nucleic Acids Rese 28:250-253
-
(2000)
MODBASE, a Database of Annotated Comparitive Protein Structure Models Nucleic Acids Rese
, vol.28
, pp. 250-253
-
-
Sanchez, R.1
Pieper, U.2
Mirkovic, N.3
Bakker, P.D.4
Wittenstein, E.5
Sali, A.6
-
63
-
-
0031307019
-
Evaluation of comparative protein structure modelling by MODELLER-3
-
Sanchez R, Sali A (1997) Evaluation of comparative protein structure modelling by MODELLER-3. Proteins Suppl 1:50-58
-
(1997)
Proteins Suppl
, vol.1
, pp. 50-58
-
-
Sanchez, R.1
Sali, A.2
-
64
-
-
0032506030
-
Large scale structure modelling of the Saccharomyces cerevisiae genome
-
Sanchez R, Sali A (1998) Large scale structure modelling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci 95:13597-13602
-
(1998)
Proc Natl Acad Sci
, vol.95
, pp. 13597-13602
-
-
Sanchez, R.1
Sali, A.2
-
65
-
-
9444264701
-
Neuropeptide Y and the nonpeptide antagonist BIBP 3226 share an overlapping binding site at the human Y1 receptor
-
Sautel M, Rudolf K, Wittneben H, Herzog H, Martinez R, Munoz M, Eberlein W, Engel W, Walker P, Beck-Sickinger AG (1996) Neuropeptide Y and the nonpeptide antagonist BIBP 3226 share an overlapping binding site at the human Y1 receptor. Mol Pharmacol 50:285-292
-
(1996)
Mol Pharmacol
, vol.50
, pp. 285-292
-
-
Sautel, M.1
Rudolf, K.2
Wittneben, H.3
Herzog, H.4
Martinez, R.5
Munoz, M.6
Eberlein, W.7
Engel, W.8
Walker, P.9
Beck-Sickinger, A.G.10
-
66
-
-
0027933763
-
Locating ligand-binding sites in 7TM receptors by protein engineering
-
Schwartz TW (1994) Locating ligand-binding sites in 7TM receptors by protein engineering. Curr Opin Biotechnol 5:434-444
-
(1994)
Curr Opin Biotechnol
, vol.5
, pp. 434-444
-
-
Schwartz, T.W.1
-
67
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi J, Blundell TL, 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
-
68
-
-
0036169280
-
The binding site of aminergic G protein-coupled receptors: The transmembrane segments and second extracellular loop
-
Shi L, Javitch JA (2002) The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol 42:437-467
-
(2002)
Annu Rev Pharmacol Toxicol
, vol.42
, pp. 437-467
-
-
Shi, L.1
Javitch, J.A.2
-
69
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209-225
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
70
-
-
0035830958
-
Prospects for ab initio protein structural genomics
-
Simons KT, Strauss C, Baker D (2001) Prospects for ab initio protein structural genomics. J Mol Biol 306:1191-1199
-
(2001)
J Mol Biol
, vol.306
, pp. 1191-1199
-
-
Simons, K.T.1
Strauss, C.2
Baker, D.3
-
71
-
-
0026704815
-
Detection of native like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations
-
Sippl M, Weitckus S (1992) Detection of native like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins 13:258-271
-
(1992)
Proteins
, vol.13
, pp. 258-271
-
-
Sippl, M.1
Weitckus, S.2
-
72
-
-
0034060287
-
Structural genomics and its importance for gene function analysis
-
Skolnick J, Fetrow JS, Kolinski A (2000) Structural genomics and its importance for gene function analysis. Nat Biotechnol 18:283-287
-
(2000)
Nat Biotechnol
, vol.18
, pp. 283-287
-
-
Skolnick, J.1
Fetrow, J.S.2
Kolinski, A.3
-
73
-
-
0035866002
-
Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
-
Skolnick J, Kihara D (2001) Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins: Struct Funct Genet 42:319-331
-
(2001)
Proteins: Struct Funct Genet
, vol.42
, pp. 319-331
-
-
Skolnick, J.1
Kihara, D.2
-
74
-
-
3142764482
-
Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm
-
Skolnick J, Kihara D, Zhang Y (2004a) Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm. Proteins 56:502-518
-
(2004)
Proteins
, vol.56
, pp. 502-518
-
-
Skolnick, J.1
Kihara, D.2
Zhang, Y.3
-
75
-
-
3142764482
-
Development and large scale benchmark testing of the Prospector-3 threading algorithm
-
Skolnick J, Kihara D, Zhang Y (2004b) Development and large scale benchmark testing of the Prospector-3 threading algorithm. Proteins 56:502-518
-
(2004)
Proteins
, vol.56
, pp. 502-518
-
-
Skolnick, J.1
Kihara, D.2
Zhang, Y.3
-
76
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195-197
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
77
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Soding, J.1
-
78
-
-
0242330730
-
Assesment of homology based predictions in CASP 5
-
Tramontano A, Morea V (2003) Assesment of homology based predictions in CASP 5. Proteins 53(Suppl 6):352-368
-
(2003)
Proteins
, vol.53
, pp. 352-368
-
-
Tramontano, A.1
Morea, V.2
-
80
-
-
0029973830
-
Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
-
Wallace AC, Laskowski RA, Thornton JM (1996) Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 5:1001-1013
-
(1996)
Protein Sci
, vol.5
, pp. 1001-1013
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
81
-
-
47949129742
-
Structure of a beta1-adrenergic G-protein-coupled receptor
-
Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, Schertler GF (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454(7203):486-491
-
(2008)
Nature
, vol.454
, Issue.7203
, pp. 486-491
-
-
Warne, T.1
Serrano-Vega, M.J.2
Baker, J.G.3
Moukhametzianov, R.4
Edwards, P.C.5
Henderson, R.6
Leslie, A.G.7
Tate, C.G.8
Schertler, G.F.9
-
83
-
-
0031720889
-
Genomics in the real world
-
Wiley SR (1998) Genomics in the real world. Curr Pharm Des 4:417-422
-
(1998)
Curr Pharm des
, vol.4
, pp. 417-422
-
-
Wiley, S.R.1
-
84
-
-
34249869832
-
Ab initio modelling of small proteins by iterative TASSER simulations
-
Wu S, Skolnick J, Zhang Y (2007a) Ab initio modelling of small proteins by iterative TASSER simulations. BMC Biol 5:17
-
(2007)
BMC Biol
, vol.5
, pp. 17
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
85
-
-
34250851687
-
LOMETS: A local meta-threading-server for protein structure prediction
-
Wu S, Zhang Y (2007b) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35(10):3375-3382
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.10
, pp. 3375-3382
-
-
Wu, S.1
Zhang, Y.2
-
86
-
-
41349114023
-
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
-
Wu S, Zhang Y (2008a) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 24:924-931
-
(2008)
Bioinformatics
, vol.24
, pp. 924-931
-
-
Wu, S.1
Zhang, Y.2
-
87
-
-
46449123146
-
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
-
Wu S, Zhang Y (2008b) MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72:547-556
-
(2008)
Proteins
, vol.72
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
89
-
-
0034663738
-
Protein threading using PROSPECT: Design and evaluation
-
Xu Y, Xu D (2000) Protein threading using PROSPECT: design and evaluation. Proteins 40:343-354
-
(2000)
Proteins
, vol.40
, pp. 343-354
-
-
Xu, Y.1
Xu, D.2
-
90
-
-
0030627408
-
Similarities and differences between nonhomologous proteins with similar folds: Evaluation of threading strategies
-
Zhang B, Jaroszewski L, Rychlewski L, Godzik A (1997) Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des 2:307-317
-
(1997)
Fold des
, vol.2
, pp. 307-317
-
-
Zhang, B.1
Jaroszewski, L.2
Rychlewski, L.3
Godzik, A.4
-
91
-
-
36749061828
-
Template-based modeling and free modeling by I-TASSER in CASP7
-
Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8):108-117
-
(2007)
Proteins
, vol.69
, pp. 108-117
-
-
Zhang, Y.1
-
92
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y (2008a) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
93
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Zhang Y (2008b) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18:342-348
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 342-348
-
-
Zhang, Y.1
-
94
-
-
74249106219
-
I-TASSER: Fully automated protein structure prediction in CASP8
-
In press
-
Zhang Y (2009a) I-TASSER: fully automated protein structure prediction in CASP8. Proteins: In press
-
(2009)
Proteins
-
-
Zhang, Y.1
-
95
-
-
64549115839
-
Protein structure prediction: When is it useful?
-
Zhang Y (2009b) Protein structure prediction: when is it useful? Curr Opin Struct Biol 19:145-155
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 145-155
-
-
Zhang, Y.1
-
96
-
-
33645793799
-
Structure modeling of all identified G protein-coupled receptors in the human genome
-
Zhang Y, Devries ME, Skolnick J (2006a) Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol 2:e13
-
(2006)
PLoS Comput Biol
, vol.2
, pp. e13
-
-
Zhang, Y.1
Devries, M.E.2
Skolnick, J.3
-
97
-
-
33644553089
-
On the origin and highly likely completeness of single-domain protein structures
-
Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J (2006b) On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci USA 103:2605-2610
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 2605-2610
-
-
Zhang, Y.1
Hubner, I.A.2
Arakaki, A.K.3
Shakhnovich, E.4
Skolnick, J.5
-
98
-
-
0036681386
-
Local energy landscape flattening: Parallel hyperbolic Monte-Carlo sampling of protein folding
-
Zhang Y, Kihara D, Skolnick J (2002) Local energy landscape flattening: Parallel hyperbolic Monte-Carlo sampling of protein folding. Proteins 48:192-201
-
(2002)
Proteins
, vol.48
, pp. 192-201
-
-
Zhang, Y.1
Kihara, D.2
Skolnick, J.3
-
99
-
-
0041843696
-
TOUCHSTONE II: A new approach to ab initio protein structure prediction
-
Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85:1145-1164
-
(2003)
Biophys J
, vol.85
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
-
100
-
-
2442676589
-
Automated Structure prediction of weekly homologous proteins on a genomic scale
-
Zhang Y, Skolnick J (2004a) Automated Structure prediction of weekly homologous proteins on a genomic scale. Proc Natl Acad Sci 101:7594-7599
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
101
-
-
1942519275
-
Spicker: Approach to clustering protein structures for near native model selection
-
Zhang Y, Skolnick J (2004b) Spicker: approach to clustering protein structures for near native model selection. J Comp Chem 25:865-871
-
(2004)
J Comp Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
102
-
-
16644386061
-
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
-
Zhang Y, Skolnick J (2004c) Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 87:2647-2655
-
(2004)
Biophys J
, vol.87
, pp. 2647-2655
-
-
Zhang, Y.1
Skolnick, J.2
-
103
-
-
12844288890
-
The protein structure prediction problem could be solved using the current PDB library
-
Zhang Y, Skolnick J (2005a) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102:1029-1034
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 1029-1034
-
-
Zhang, Y.1
Skolnick, J.2
-
104
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J (2005b) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302-2309
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
105
-
-
2542631929
-
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
-
Zhou H, Zhou Y (2004) Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 55:1005-1013
-
(2004)
Proteins
, vol.55
, pp. 1005-1013
-
-
Zhou, H.1
Zhou, Y.2
-
106
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58:321-328
-
(2005)
Proteins
, vol.58
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
-
107
-
-
0028031727
-
A reciprocal mutation supports helix 2 and helix 7 proximity in the gonadotropinreleasing hormone receptor
-
Zhou W, Flanagan C, Ballesteros JA, Konvicka K, Davidson JS, Weinstein H, Millar RP, Sealfon SC (1994) A reciprocal mutation supports helix 2 and helix 7 proximity in the gonadotropinreleasing hormone receptor. Mol Pharmacol 45:165-170
-
(1994)
Mol Pharmacol
, vol.45
, pp. 165-170
-
-
Zhou, W.1
Flanagan, C.2
Ballesteros, J.A.3
Konvicka, K.4
Davidson, J.S.5
Weinstein, H.6
Millar, R.P.7
Sealfon, S.C.8
|