-
1
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
Berman, H.M., Henrick, K. and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
-
(2003)
Nat. Struct. Biol
, vol.10
, pp. 980
-
-
Berman, H.M.1
Henrick, K.2
Nakamura, H.3
-
2
-
-
0017411710
-
Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
-
(1977)
J. Mol. Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer Jr., E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
3
-
-
0033924043
-
AutoDep: A web-based system for deposition and validation of macromolecular structural information
-
Lin, D., Manning, N.O., Jiang, J., Abola, E.E., Stampf, D., Prilusky, J. and Sussman, J.L. (2000) AutoDep: A web-based system for deposition and validation of macromolecular structural information. Acta Cryst. D, D56, 828-841.
-
(2000)
Acta Cryst. D
, vol.D56
, pp. 828-841
-
-
Lin, D.1
Manning, N.O.2
Jiang, J.3
Abola, E.E.4
Stampf, D.5
Prilusky, J.6
Sussman, J.L.7
-
4
-
-
0032215435
-
Deposition of macromolecular structures
-
Keller, P.A., Henrick, K., McNeil, P., Moodie, S. and Barton, G.J. (1998) Deposition of macromolecular structures. Acta Crystallogr. D Biol. Crystallogr., 1105-1108.
-
(1998)
Acta Crystallogr. D Biol. Crystallogr
, pp. 1105-1108
-
-
Keller, P.A.1
Henrick, K.2
McNeil, P.3
Moodie, S.4
Barton, G.J.5
-
5
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (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
-
-
38549137908
-
-
Dutta, S., Burkhardt, K., Bluhm, W.F. and Berman, H.M. (2005) Using the tools and resources of the RCSB Protein Data Bank. Current Protocols in Bioinformatics, 1.9.1-1.9.40.
-
Dutta, S., Burkhardt, K., Bluhm, W.F. and Berman, H.M. (2005) Using the tools and resources of the RCSB Protein Data Bank. Current Protocols in Bioinformatics, 1.9.1-1.9.40.
-
-
-
-
7
-
-
0037264585
-
The PDB format, mmCIF formats and other data formats
-
Bourne, P.E. and Weissig, H, eds, John Wiley & Sons, Inc, NJ, Hoboken, pp
-
Westbrook, J. and Fitzgerald, P.M. (2003) The PDB format, mmCIF formats and other data formats. In Bourne, P.E. and Weissig, H. (eds), Structural Bioinformatics, John Wiley & Sons, Inc., NJ, Hoboken, pp. 161-179.
-
(2003)
Structural Bioinformatics
, pp. 161-179
-
-
Westbrook, J.1
Fitzgerald, P.M.2
-
8
-
-
0023965741
-
SMILES 1. Introduction and encoding rules
-
Weininger, D. (1988) SMILES 1. Introduction and encoding rules. J. Chem. Inf. Comput. Sci., 28, 31.
-
(1988)
J. Chem. Inf. Comput. Sci
, vol.28
, pp. 31
-
-
Weininger, D.1
-
9
-
-
38549102078
-
-
©The International Union of Pure and Applied Chemistry. (2005) IUPAC International Chemical Identifier (InChI) (contact: secretariatιupac.org)
-
©The International Union of Pure and Applied Chemistry. (2005) IUPAC International Chemical Identifier (InChI) (contact: secretariatιupac.org)
-
-
-
-
10
-
-
0032110340
-
Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task G-roup on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy
-
Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K. (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task G-roup on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J. Biomol. NMR. 12, 1-23.
-
(1998)
J. Biomol. NMR
, vol.12
, pp. 1-23
-
-
Markley, J.L.1
Bax, A.2
Arata, Y.3
Hilbers, C.W.4
Kaptein, R.5
Sykes, B.D.6
Wright, P.E.7
Wüthrich, K.8
-
11
-
-
0035173371
-
The PDB data uniformity project
-
Bhat, T.N., Bourne, P., Feng, Z., Gilliland, G., Jain, S., Ravichandran, V., Schneider, B., Schneider, K., Thanki, N., Weissig, H. et al. (2001) The PDB data uniformity project. Nucleic Acids Res., 29 214-218.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 214-218
-
-
Bhat, T.N.1
Bourne, P.2
Feng, Z.3
Gilliland, G.4
Jain, S.5
Ravichandran, V.6
Schneider, B.7
Schneider, K.8
Thanki, N.9
Weissig, H.10
-
12
-
-
33846041078
-
The universal protein resource (UniProt)
-
The UniProt Consortium
-
The UniProt Consortium. (2007) The universal protein resource (UniProt). Nucleic Acids Res, 35, D193-D197.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
-
13
-
-
13444288174
-
E-MSD: An integrated data resource for bioinformatics
-
Velankar, S., McNeiI, P., Mittard-Runte, V., Suarez, A., Barrell, D., Apweiler, R. and Henrick, K. (2005) E-MSD: An integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Velankar, S.1
McNeiI, P.2
Mittard-Runte, V.3
Suarez, A.4
Barrell, D.5
Apweiler, R.6
Henrick, K.7
-
14
-
-
0037110896
-
CHIMERA: A software tool for reaction rate calculations and kinetics and thermodynamics analysis
-
Novoselov, K.P., Shirabaikin, D.B., Umanskii, S.Y., Vladimirov, A.S., Minushev, A. and Korkin, A.A. (2002) CHIMERA: A software tool for reaction rate calculations and kinetics and thermodynamics analysis. J. Comput. Chem., 23, 1375-1389.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1375-1389
-
-
Novoselov, K.P.1
Shirabaikin, D.B.2
Umanskii, S.Y.3
Vladimirov, A.S.4
Minushev, A.5
Korkin, A.A.6
-
15
-
-
33644873919
-
VIPERdb: A relational database for structural virology
-
Shepherd, C.M., Borelli, LA., Lander, G., Natarajaa, P., Siddavanahalli, V., Bajaj, C., Johnson, J.E., Brooks, C.L. III and Reddy, V.S. (2006) VIPERdb: A relational database for structural virology. Nucleic Acids Res., 34, D386-D389.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Shepherd, C.M.1
Borelli, L.A.2
Lander, G.3
Natarajaa, P.4
Siddavanahalli, V.5
Bajaj, C.6
Johnson, J.E.7
Brooks III, C.L.8
Reddy, V.S.9
-
16
-
-
0032169688
-
PQS: A protein quarternary file server
-
Henrick, K. and Thornton, J.M. (1998) PQS: A protein quarternary file server. Trends Biochem. Sci., 23, 358-361.
-
(1998)
Trends Biochem. Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
17
-
-
0032922193
-
SFCHECK: A unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model
-
Vaguine, A.A., Richelle, J. and Wodak, S.J. (1999) SFCHECK: A unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D Biol. Crystallogr., 55, 191-205.
-
(1999)
Acta Crystallogr. D Biol. Crystallogr
, vol.55
, pp. 191-205
-
-
Vaguine, A.A.1
Richelle, J.2
Wodak, S.J.3
-
18
-
-
14644420979
-
The Uppsala electron-density server
-
Kleywegt, G.J., Harris, M.R., Zou, J.Y., Taylor, T.C., Wahlby, A. and Jones, T.A. (2004) The Uppsala electron-density server. Acta Crystallogr. D Biol. Crystallogr., 60, 2240-2249.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr
, vol.60
, pp. 2240-2249
-
-
Kleywegt, G.J.1
Harris, M.R.2
Zou, J.Y.3
Taylor, T.C.4
Wahlby, A.5
Jones, T.A.6
-
19
-
-
0006586449
-
-
Brookhaven National Laboratory
-
Cailaway, J., Cummings, M., Deroski, B., Esposito, P., Forman, A., Langdon, P., Libeson, ML, McCarthy, J., Sikora, J., Xue, D. et al. (1996) Protein data bank contents guide: Atomic coordinate entry formal description. Brookhaven National Laboratory.
-
(1996)
Protein data bank contents guide: Atomic coordinate entry formal description
-
-
Cailaway, J.1
Cummings, M.2
Deroski, B.3
Esposito, P.4
Forman, A.5
Langdon, P.6
Libeson, M.L.7
McCarthy, J.8
Sikora, J.9
Xue, D.10
-
20
-
-
33645465078
-
Definition and exchange of crystallographic data
-
Hall, S.R. and McMahon, B, eds, Springer, Dordrecht, The Netherlands
-
Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P,E., McMahon, B., Watanpaugh, K.D. and Berman, H.M. (2005) Definition and exchange of crystallographic data. In Hall, S.R. and McMahon, B. (eds), International Tables for Crystallography, Springer, Dordrecht, The Netherlands, Vol. G, pp. 295-443.
-
(2005)
International Tables for Crystallography
, vol.G
, pp. 295-443
-
-
Fitzgerald, P.M.D.1
Westbrook, J.D.2
Bourne, P.E.3
McMahon, B.4
Watanpaugh, K.D.5
Berman, H.M.6
-
21
-
-
33746986976
-
Definition and exchange of crystallographic, data
-
Hall, S.R. and McMahon, B, eds, Springer, Dordrecht, The Netherlands
-
Westbrook, J., Henrick, K., Ulrich, E.L. and Berman, H.M. (2005) Definition and exchange of crystallographic, data. In Hall, S.R. and McMahon, B. (eds), International Tables for Crystallography, Springer, Dordrecht, The Netherlands, Vol. G, pp. 195-198.
-
(2005)
International Tables for Crystallography
, vol.G
, pp. 195-198
-
-
Westbrook, J.1
Henrick, K.2
Ulrich, E.L.3
Berman, H.M.4
-
22
-
-
16344364140
-
PDBML: The representation of archival macromolecular. structure data in XML
-
Westbrook, J., Ito, N., Nakamura, H., Henrick, K. and Berman, H.M. (2005) PDBML: The representation of archival macromolecular. structure data in XML. Bioinformatics, 21, 988-992.
-
(2005)
Bioinformatics
, vol.21
, pp. 988-992
-
-
Westbrook, J.1
Ito, N.2
Nakamura, H.3
Henrick, K.4
Berman, H.M.5
-
23
-
-
9144231249
-
-
E-MSD: An integrated data resource for bioinformatics, Database issue, D211-D216
-
Golovin, A., Oldfield, TJ., Tate, J.G., Velankar, S., Barton, G.J., Boutselakis, H., Dimitropoulos, D., Fillon, J., Hussain, A., Ionides, J.M. et al. (2004) E-MSD: An integrated data resource for bioinformatics. Nucleic Acids Res., 32(Database issue), D211-D216.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Golovin, A.1
Oldfield, T.J.2
Tate, J.G.3
Velankar, S.4
Barton, G.J.5
Boutselakis, H.6
Dimitropoulos, D.7
Fillon, J.8
Hussain, A.9
Ionides, J.M.10
-
24
-
-
0028336046
-
Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and flexibility
-
Ihlenfeldt, W., Takahasi, Y., Abe, H. and Sasaki, S. (1994) Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and flexibility. J. Chem. Inf. Comp. Sci. 34, 109-116.
-
(1994)
J. Chem. Inf. Comp. Sci
, vol.34
, pp. 109-116
-
-
Ihlenfeldt, W.1
Takahasi, Y.2
Abe, H.3
Sasaki, S.4
-
25
-
-
38549159530
-
-
OpenEye Scientific Software Inc, 2007 OpenEye OEChem version 1.5, Santa Fe, NM, USA
-
OpenEye Scientific Software Inc. (2007) OpenEye OEChem version 1.5, www.eyesopen.com Santa Fe, NM, USA
-
-
-
-
26
-
-
13244253766
-
pdb-care t (PDB carbohydrate residue check): A program to support annotation of complex carbohydrate structures in PDB files
-
Lutteke, T. and von der Lieth, C.W. (2004) pdb-care t (PDB carbohydrate residue check): A program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics, 5, 69.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 69
-
-
Lutteke, T.1
von der Lieth, C.W.2
-
27
-
-
31444452744
-
Automatic generation of 3D-atomic coordinates for organic molecules
-
Gasteiger, J., Rudolph, C. and Sadowski, J. (1990) Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comp. Method, 3, 537-547.
-
(1990)
Tetrahedron Comp. Method
, vol.3
, pp. 537-547
-
-
Gasteiger, J.1
Rudolph, C.2
Sadowski, J.3
-
28
-
-
38549098604
-
-
OpenEye Scientific Software Inc, 2007 OpenEye Omega version 2.2.1, Santa Fe, NM, USA
-
OpenEye Scientific Software Inc. (2007) OpenEye Omega version 2.2.1, www.eyesopen.com Santa Fe, NM, USA
-
-
-
-
29
-
-
38549166695
-
-
Advanced Chemistry Development, I, 2007 ACD/Name Batch, version 9.0, Toronto ON, Canada
-
Advanced Chemistry Development, I. (2007) ACD/Name Batch, version 9.0, Toronto ON, Canada, www.acdlabs.com
-
-
-
-
30
-
-
0013462042
-
BALI: Automatic assignment of bond and atom types for protein ligands in the Brookhaven Protein Databank
-
Hendlich, M., Rippmann, F. and Barnickel, G. (1997) BALI: Automatic assignment of bond and atom types for protein ligands in the Brookhaven Protein Databank. J. Chem. Inf. Comp. Sci. 37, 774-778.
-
(1997)
J. Chem. Inf. Comp. Sci
, vol.37
, pp. 774-778
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
31
-
-
33745359822
-
The blue obelisk-interoperability in chemical informatics
-
Guha, R., Howard, M.T., Hutchison, G.R., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J. and Willighagen, E.L. (2006) The blue obelisk-interoperability in chemical informatics. J. Chem. Inf. Model 46, 991-998.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 991-998
-
-
Guha, R.1
Howard, M.T.2
Hutchison, G.R.3
Murray-Rust, P.4
Rzepa, H.5
Steinbeck, C.6
Wegner, J.7
Willighagen, E.L.8
-
32
-
-
38549164242
-
-
The Open Babel Package, 2006 Version 2.0.1
-
The Open Babel Package. (2006) Version 2.0.1 http://openbabel.sourceforge.net/
-
-
-
-
33
-
-
0346753470
-
Validation of protein structures for the Protein Data Bank
-
Westbrook, J., Feng, Z., Burkhardt, K. and Berman, H.M. (2003) Validation of protein structures for the Protein Data Bank. Meth. Enz., 374, 370-385.
-
(2003)
Meth. Enz
, vol.374
, pp. 370-385
-
-
Westbrook, J.1
Feng, Z.2
Burkhardt, K.3
Berman, H.M.4
-
35
-
-
0034284122
-
Recent changes to RasMol, recombining the variants
-
Bernstein, H.J. (2000) Recent changes to RasMol, recombining the variants. Trends Biochem. Sci., 25, 453-455.
-
(2000)
Trends Biochem. Sci
, vol.25
, pp. 453-455
-
-
Bernstein, H.J.1
-
38
-
-
0030814038
-
WebMol-a Java-based PDB viewer
-
Walther, D. (1997) WebMol-a Java-based PDB viewer. Trends Biochem. Sci., 22, 274-275.
-
(1997)
Trends Biochem. Sci
, vol.22
, pp. 274-275
-
-
Walther, D.1
-
39
-
-
32044456003
-
The backrub motion: How protein backbone shrugs when a sidechain dances
-
Davis, I.W., Arendall, W.B. III, Richardson, D.C. and Richardson, J.S. (2006) The backrub motion: How protein backbone shrugs when a sidechain dances. Structure, 14, 265-274.
-
(2006)
Structure
, vol.14
, pp. 265-274
-
-
Davis, I.W.1
Arendall III, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
40
-
-
25444436686
-
The molecular biology toolkit (MBT): A modular platform for developing molecular visualization applications
-
Moreland, J.L., Gramada, A., Buzko, O.V., Zhang, Q. and Bourne, P.E. (2005) The molecular biology toolkit (MBT): A modular platform for developing molecular visualization applications. BMC Bioinformatics 6, 21.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 21
-
-
Moreland, J.L.1
Gramada, A.2
Buzko, O.V.3
Zhang, Q.4
Bourne, P.E.5
-
41
-
-
3042683893
-
eF-site and PDBjViewer: Database and viewer for protein functional sites
-
Kinoshita, K. and Nakamura, H. (2004) eF-site and PDBjViewer: Database and viewer for protein functional sites. Bioinformatics, 20, 1329-1330.
-
(2004)
Bioinformatics
, vol.20
, pp. 1329-1330
-
-
Kinoshita, K.1
Nakamura, H.2
-
42
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
|