-
4
-
-
84861425552
-
Linking crystallographic model and data quality
-
Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336:1030-1033
-
(2012)
Science
, vol.336
, pp. 1030-1033
-
-
Karplus, P.A.1
Diederichs, K.2
-
5
-
-
79952608525
-
Accurate bond and angle parameters for X-ray protein-structure refi nement
-
Engh RA, Huber R (1991) Accurate bond and angle parameters for X-ray protein-structure refi nement. Acta Crystallogr A 47:392-400
-
(1991)
Acta Crystallogr A
, vol.47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
6
-
-
84873572846
-
Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures
-
Pozharski E, Weichenberger CX, Rupp B (2013) Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta Crystallogr D 69:150-167
-
(2013)
Acta Crystallogr D
, vol.69
, pp. 150-167
-
-
Pozharski, E.1
Weichenberger, C.X.2
Rupp, B.3
-
7
-
-
0000243829
-
PROCHECK - A program to check the stereochemical quality of protein structures
-
Laskowski RA, MacArthur MW, Moss DS et al (1993) PROCHECK-a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291
-
(1993)
J Appl Crystallogr
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
-
9
-
-
0027081912
-
SQUID: A program for the analysis and display of data from crystallography and molecular dynamics
-
Oldfield TJ (1992) SQUID: a program for the analysis and display of data from crystallography and molecular dynamics. J Mol Graph 10:247-252
-
(1992)
J Mol Graph
, vol.10
, pp. 247-252
-
-
Oldfield, T.J.1
-
10
-
-
0030598343
-
Deviations from standard atomic volumes as a quality measure for protein crystal structures
-
Pontius J, Richelle J, Wodak SJ (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 264:121-136
-
(1996)
J Mol Biol
, vol.264
, pp. 121-136
-
-
Pontius, J.1
Richelle, J.2
Wodak, S.J.3
-
11
-
-
0032922193
-
SFCHECK: A unifi ed set of procedures for evaluating the quality of macromolecular structurefactor data and their agreement with the atomic model
-
Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unifi ed set of procedures for evaluating the quality of macromolecular structurefactor data and their agreement with the atomic model. Acta Crystallogr D 55:191-205
-
(1999)
Acta Crystallogr D
, vol.55
, pp. 191-205
-
-
Vaguine, A.A.1
Richelle, J.2
Wodak, S.J.3
-
12
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB III, Headd JJ et al (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D 66:12-21
-
(2010)
Acta Crystallogr D
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall Iii., W.B.2
Headd, J.J.3
-
13
-
-
16644393507
-
Automated and accurate deposition of structures solved by X-ray diffraction to the protein data bank
-
Yang HW, Guranovic V, Dutta S et al (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the protein data bank. Acta Crystallogr D 60:1833-1839
-
(2004)
Acta Crystallogr D
, vol.60
, pp. 1833-1839
-
-
Yang, H.W.1
Guranovic, V.2
Dutta, S.3
-
14
-
-
0027207221
-
Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
-
Colloc'h N, Etchebest C, Thoreau E et al (1993) Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng 6:377-382
-
(1993)
Protein Eng
, vol.6
, pp. 377-382
-
-
Colloc'H, N.1
Etchebest, C.2
Thoreau, E.3
-
16
-
-
77954290877
-
PROSESS: A protein structure evaluation suite and server
-
Berjanskii M, Liang Y, Zhou J et al (2010) PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res 38:W633-W640
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Berjanskii, M.1
Liang, Y.2
Zhou, J.3
-
17
-
-
78651250896
-
Challenges in the determination of the binding modes of nonstandard ligands in X-ray crystal complexes
-
Malde AK, Mark AE (2011) Challenges in the determination of the binding modes of nonstandard ligands in X-ray crystal complexes. J Comput Aided Mol Des 25:1-12
-
(2011)
J Comput Aided Mol des
, vol.25
, pp. 1-12
-
-
Malde, A.K.1
Mark, A.E.2
-
18
-
-
0001752768
-
The cambridge structural database: A quarter of a million crystal structures and rising
-
Allen FH (2002) The cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr B 58:380-388
-
(2002)
Acta Crystallogr B
, vol.58
, pp. 380-388
-
-
Allen, F.H.1
-
19
-
-
84860290638
-
JLigand: A graphical tool for the CCP4 template-restraint library
-
Lebedev AA, Young P, Isupov MN et al (2012) JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr D 68:431-440
-
(2012)
Acta Crystallogr D
, vol.68
, pp. 431-440
-
-
Lebedev, A.A.1
Young, P.2
Isupov, M.N.3
-
20
-
-
84870574242
-
Assessing the accuracy of templatebased structure prediction metaservers by comparison with structural genomics structures
-
Gront D, Grabowski M, Zimmerman MD et al (2012) Assessing the accuracy of templatebased structure prediction metaservers by comparison with structural genomics structures. J Struct Funct Genomics 13:213-225
-
(2012)
J Struct Funct Genomics
, vol.13
, pp. 213-225
-
-
Gront, D.1
Grabowski, M.2
Zimmerman, M.D.3
-
21
-
-
56649091319
-
PURY: A database of geometric restraints of hetero compounds for refi nement in complexes with macromolecular structures
-
Andrejasic M, Praaenikar J, Turk D (2008) PURY: a database of geometric restraints of hetero compounds for refi nement in complexes with macromolecular structures. Acta Crystallogr D 64:1093-1109
-
(2008)
Acta Crystallogr D
, vol.64
, pp. 1093-1109
-
-
Andrejasic, M.1
Praaenikar, J.2
Turk, D.3
-
22
-
-
33745933955
-
HKL-3000: The integration of data reduction and structure solution-from diffraction images to an initial model in minutes
-
Minor W, Cymborowski M, Otwinowski Z et al (2006) HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes. Acta Crystallogr D 62:859-866
-
(2006)
Acta Crystallogr D
, vol.62
, pp. 859-866
-
-
Minor, W.1
Cymborowski, M.2
Otwinowski, Z.3
-
23
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
29
-
Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52-56, 29
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
24
-
-
0027304152
-
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
-
Brunne RM, Liepinsh E, Otting G et al (1993) Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol 231:1040-1048
-
(1993)
J Mol Biol
, vol.231
, pp. 1040-1048
-
-
Brunne, R.M.1
Liepinsh, E.2
Otting, G.3
-
25
-
-
84957316785
-
Proton-exchange with internal water molecules in the protein BPTI in aqueous-solution
-
Otting G, Liepinsh E, Wüthrich K (1991) Proton-exchange with internal water molecules in the protein BPTI in aqueous-solution. J Am Chem Soc 113:4363-4364
-
(1991)
J Am Chem Soc
, vol.113
, pp. 4363-4364
-
-
Otting, G.1
Liepinsh, E.2
Wüthrich, K.3
-
26
-
-
0029889510
-
The dynamics of water-protein interactions
-
Bryant RG (1996) The dynamics of water-protein interactions. Annu Rev Biophys Biomol Struct 25:29-53
-
(1996)
Annu Rev Biophys Biomol Struct
, vol.25
, pp. 29-53
-
-
Bryant, R.G.1
-
27
-
-
0033081137
-
How many water molecules can be detected by protein crystallography?
-
Carugo O, Bordo D (1999) How many water molecules can be detected by protein crystallography? Acta Crystallogr D 55: 479-483
-
(1999)
Acta Crystallogr D
, vol.55
, pp. 479-483
-
-
Carugo, O.1
Bordo, D.2
-
28
-
-
37349016530
-
Protein crystallography for noncrystallographers, or how to get the best (but not more) from published macromolecular structures
-
Wlodawer A, Minor W, Dauter Z et al (2008) Protein crystallography for noncrystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275:1-21
-
(2008)
FEBS J
, vol.275
, pp. 1-21
-
-
Wlodawer, A.1
Minor, W.2
Dauter, Z.3
-
29
-
-
84860284066
-
PDB REDO: Constructive validation, more than just looking for errors
-
Joosten RP, Joosten K, Murshudov GN et al (2012) PDB REDO: constructive validation, more than just looking for errors. Acta Crystallogr D 68:484-496
-
(2012)
Acta Crystallogr D
, vol.68
, pp. 484-496
-
-
Joosten, R.P.1
Joosten, K.2
Murshudov, G.N.3
-
30
-
-
2142689200
-
SOLVE and RESOLVE: Automated structure solution, density modifi-cation, and model building
-
Terwilliger T (2004) SOLVE and RESOLVE: automated structure solution, density modifi-cation, and model building. J Synchrotron Radiat 11:49-52
-
(2004)
J Synchrotron Radiat
, vol.11
, pp. 49-52
-
-
Terwilliger, T.1
-
31
-
-
0032964481
-
Automated protein model building combined with iterative structure refi nement
-
Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refi nement. Nat Struct Biol 6:458-463
-
(1999)
Nat Struct Biol
, vol.6
, pp. 458-463
-
-
Perrakis, A.1
Morris, R.2
Lamzin, V.S.3
-
32
-
-
0038793604
-
Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modifi cation and refi nement
-
Terwilliger TC (2003) Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modifi cation and refi nement. Acta Crystallogr D 59:1174-1182
-
(2003)
Acta Crystallogr D
, vol.59
, pp. 1174-1182
-
-
Terwilliger, T.C.1
-
33
-
-
84860752223
-
Fragmentation-tree density representation for crystallographic modelling of bound ligands
-
Langer GG, Evrard GX, Carolan CG et al (2012) Fragmentation-tree density representation for crystallographic modelling of bound ligands. J Mol Biol 419:211-222
-
(2012)
J Mol Biol
, vol.419
, pp. 211-222
-
-
Langer, G.G.1
Evrard, G.X.2
Carolan, C.G.3
-
34
-
-
76449098262
-
PHENIX: A comprehensive pythonbased system for macromolecular structure solution
-
Adams PD, Afonine PV, Bunkoczi G et al (2010) PHENIX: a comprehensive pythonbased system for macromolecular structure solution. Acta Crystallogr D 66:213-221
-
(2010)
Acta Crystallogr D
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkoczi, G.3
-
35
-
-
84891787533
-
-
Accessed 23 Apr 2013
-
de Beer TA (2013) LigSearch. http://www.ebi.ac.uk/thornton-srv/databases/ LigSearch/index.html. Accessed 23 Apr 2013
-
(2013)
Lig Search
-
-
De Beer, T.A.1
-
36
-
-
84866648571
-
Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes
-
Perkins A, Gretes MC, Nelson KJ et al (2012) Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes. Biochemistry 51:7638-7650
-
(2012)
Biochemistry
, vol.51
, pp. 7638-7650
-
-
Perkins, A.1
Gretes, M.C.2
Nelson, K.J.3
-
37
-
-
0025977709
-
Crystal structure of interleukin 8: Symbiosis of NMR and crystallography
-
Baldwin ET, Weber IT, St Charles R et al (1991) Crystal structure of interleukin 8: symbiosis of NMR and crystallography. Proc Natl Acad Sci USA 88:502-506
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 502-506
-
-
Baldwin, E.T.1
Weber, I.T.2
St Charles, R.3
-
38
-
-
62949126043
-
Improving NMR protein structure quality by rosetta refi nement: A molecular replacement study
-
Ramelot TA, Raman S, Kuzin AP et al (2009) Improving NMR protein structure quality by rosetta refi nement: a molecular replacement study. Proteins 75:147-167
-
(2009)
Proteins
, vol.75
, pp. 147-167
-
-
Ramelot, T.A.1
Raman, S.2
Kuzin, A.P.3
-
39
-
-
79957592606
-
Improved molecular replacement by densityand energy-guided protein structure optimization
-
DiMaio F, Terwilliger TC, Read RJ et al (2011) Improved molecular replacement by densityand energy-guided protein structure optimization. Nature 473:540-543
-
(2011)
Nature
, vol.473
, pp. 540-543
-
-
Dimaio, F.1
Terwilliger, T.C.2
Read, R.J.3
-
40
-
-
77955491294
-
Predicting protein structures with a multiplayer online game
-
Cooper S, Khatib F, Treuille A et al (2010) Predicting protein structures with a multiplayer online game. Nature 466:756-760
-
(2010)
Nature
, vol.466
, pp. 756-760
-
-
Cooper, S.1
Khatib, F.2
Treuille, A.3
-
41
-
-
80455154956
-
Crystal structure of a monomeric retroviral protease solved by protein folding game players
-
Foldit Contenders Group
-
Khatib F, DiMaio F, Foldit Contenders Group et al (2011) Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol 18:1175-1177
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 1175-1177
-
-
Khatib, F.1
Dimaio, F.2
-
42
-
-
80955159982
-
High-resolution structure of a retroviral protease folded as a monomer
-
Gilski M, Kazmierczyk M, Krzywda S et al (2011) High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallogr D 67:907-914
-
(2011)
Acta Crystallogr D
, vol.67
, pp. 907-914
-
-
Gilski, M.1
Kazmierczyk, M.2
Krzywda, S.3
|