-
1
-
-
84862970421
-
Protein structure validation by generalized linear model rootmean-square deviation prediction
-
doi:10.1002/pro.2007
-
Bagaria A, Jaravine V, Huang YJ, Montelione GT, Güntert P (2012) Protein structure validation by generalized linear model rootmean-square deviation prediction. Protein Sci 21(2):229-238. doi:10.1002/pro.2007
-
(2012)
Protein Sci
, vol.21
, Issue.2
, pp. 229-238
-
-
Bagaria, A.1
Jaravine, V.2
Huang, Y.J.3
Montelione, G.T.4
Güntert, P.5
-
2
-
-
76349095571
-
In defence of our science-validation now!
-
doi:10.1107/S1744309110001326
-
Baker EN, Dauter Z, Einspahr H, Weiss MS (2010) In defence of our science-validation now! Acta Crystallogr F Struct Biol Cryst Commun 66(Pt 2):112. doi:10.1107/S1744309110001326
-
(2010)
Acta Crystallogr F Struct Biol Cryst Commun
, vol.66
, Issue.PART 2
, pp. 112
-
-
Baker, E.N.1
Dauter, Z.2
Einspahr, H.3
Weiss, M.S.4
-
3
-
-
25844506708
-
Weak alignment NMR: A hawk-eyed view of biomolecular structure
-
DOI 10.1016/j.sbi.2005.08.006, PII S0959440X05001545, Carbohydrates and Glycoconjugates/Biophysical Methods
-
Bax A, Grishaev A (2005) Weak alignment NMR: A hawk-eyed view of biomolecular structure. Curr Opin Struct Biol 15(5):563-570. doi:10.1016/j.sbi.2005.08.006 (Pubitemid 41393488)
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.5
, pp. 563-570
-
-
Bax, A.1
Grishaev, A.2
-
5
-
-
79952600759
-
Cython: The best of both worlds
-
doi101109/MCSE2010118
-
Behnel S, Bradshaw R, Citro C, Dalcin L, Seljebotn DS, Smith K (2011) Cython: The best of both worlds. Comput Sci Eng 13(2):31-39. doi:10.1109/MCSE.2010.118
-
(2011)
Comput Sci Eng
, vol.13
, Issue.2
, pp. 31-39
-
-
Behnel, S.1
Bradshaw, R.2
Citro, C.3
Dalcin, L.4
Seljebotn, D.S.5
Smith, K.6
-
6
-
-
37848999781
-
Application of the random coil index to studying protein flexibility
-
doi101007/s10858-007-9208-9210
-
Berjanskii MV, Wishart DS (2008) Application of the random coil index to studying protein flexibility. J Biomol NMR 40(1):31-48. doi:10.1007/s10858-007- 9208-0
-
(2008)
J Biomol NMR
, vol.40
, Issue.1
, pp. 31-48
-
-
Berjanskii, M.V.1
Wishart, D.S.2
-
7
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
DOI 10.1038/nsb1203-980
-
Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10(12):980. doi: 10.1038/nsb1203-980 (Pubitemid 37500485)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.12
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
8
-
-
33847079676
-
Evaluating protein structures determined by structural genomics consortia
-
doi101002/rot 21165
-
Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins Struct Funct Bioinformatics 66(4):778-795. doi:10.1002/prot. 21165
-
(2007)
Proteins Struct Funct Bioinformatics
, vol.66
, Issue.4
, pp. 778-795
-
-
Bhattacharya, A.1
Tejero, R.2
Montelione, G.T.3
-
9
-
-
84865655100
-
NMR structure note: Solution structure of Ca2? binding domain 2B of the third isoform of the Na?/Ca2? exchanger
-
Breukels V, Touw W, Vuister GW (2012) NMR structure note: Solution structure of Ca2? binding domain 2B of the third isoform of the Na?/Ca2? exchanger. J Biomol NMR 54:115-121
-
(2012)
J Biomol NMR
, vol.54
, pp. 115-121
-
-
Breukels, V.1
Touw, W.2
Vuister, G.W.3
-
10
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668-1688. doi:10.1002/jcc. 20290 (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
11
-
-
29244438431
-
-
DeLano Scientific, San Carlos.
-
DeLano W, Bromberg S (2004) PyMOL user guide. DeLano Scientific, San Carlos. http://pymol.sourceforge.net/newman/ userman.pdf
-
(2004)
PyMOL User Guide
-
-
DeLano, W.1
Bromberg, S.2
-
12
-
-
0034529140
-
Disulfide recognition in an optimized threading potential
-
Dombkowski AA, Crippen GM (2000) Disulfide recognition in an optimized threading potential. Protein Eng Des Sel 13(10):679-689. doi:10.1093/protein/13. 10.679 (Pubitemid 32001376)
-
(2000)
Protein Engineering
, vol.13
, Issue.10
, pp. 679-689
-
-
Dombkowski, A.A.1
Crippen, G.M.2
-
13
-
-
0032493714
-
Quality assessment of NMR structures: A statistical survey
-
DOI 10.1006/jmbi.1998.1808
-
Doreleijers JF, Rullmann J, Kaptein R (1998) Quality assessment of NMR structures: A statistical survey. J Mol Biol 281(1):149-164. doi:10.1006/jmbi.1998.1808 (Pubitemid 28360678)
-
(1998)
Journal of Molecular Biology
, vol.281
, Issue.1
, pp. 149-164
-
-
Doreleijers, J.F.1
Rullmann, J.A.C.2
Kaptein, R.3
-
14
-
-
0032707718
-
Validation of nuclear magnetic resonance structures of proteins and nucleic acids: Hydrogen geometry and nomenclature
-
DOI 10.1002/(SICI)1097-0134(19991 115)37:3<404::AID-PROT8>3. 0.CO;2-2
-
Doreleijers JF, Vriend G, Raves ML, Kaptein R (1999) Validation of nuclear magnetic resonance structures of proteins and nucleic acids: Hydrogen geometry and nomenclature. Proteins Struct Funct Bioinformatics 37(3):404-416. doi:10.1002/(SICI)1097-0134(19991115)37:3\404:AID-PROT8[3.0.CO;2-2 (Pubitemid 29519730)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.3
, pp. 404-416
-
-
Doreleijers, J.F.1
Vriend, G.2
Raves, M.L.3
Kaptein, R.4
-
15
-
-
23144441604
-
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures
-
DOI 10.1007/s10858-005-2195-0
-
Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AMJJ, Kaptein R, Markley JL et al (2005) Bio Mag Res Bank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J Biomol NMR 32(1):1-12. doi:10.1007/ s10858-005-2195-0 (Pubitemid 41086462)
-
(2005)
Journal of Biomolecular NMR
, vol.32
, Issue.1
, pp. 1-12
-
-
Doreleijers, J.F.1
Nederveen, A.J.2
Vranken, W.3
Lin, J.4
Bonvin, A.M.J.J.5
Kaptein, R.6
Markley, J.L.7
Ulrich, E.L.8
-
16
-
-
71049172008
-
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries
-
doi101007/s10858-389-396 doi101007/s10009
-
Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW et al (2009) The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J Biomol NMR 45(4):389-396. doi:10.1007/s10858-009- 9378-z Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW (2011) NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. doi:10.1093/nar/ gkr1134
-
(2009)
J Biomol NMR
, vol.45
, Issue.4
, pp. 389-396
-
-
Doreleijers, J.F.1
Vranken, W.F.2
Schulte, C.3
Lin, J.4
Wedell, J.R.5
Penkett, C.J.6
Vuister, G.W.7
-
17
-
-
84855878395
-
Comprehensive automation for NMR structure determination of proteins
-
doi:101007/978-429-451 doi:101007/971
-
Guerry P, Herrmann T (2012) Comprehensive automation for NMR structure determination of proteins. Methods Mol Biol (Clifton, NJ) 831:429-451. doi:10.1007/978-1-61779-480-3-22
-
(2012)
Methods Mol Biol (Clifton, NJ
, vol.831
, pp. 429-451
-
-
Guerry, P.1
Herrmann, T.2
-
18
-
-
4644340524
-
Automated NMR structure calculation with CYANA
-
doi: 101385/1-353-378 doi: 10159259
-
Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol (Clifton, NJ) 278:353-378. doi: 10.1385/1-59259-809-9:353
-
(2004)
Methods Mol Biol (Clifton, NJ
, vol.278
, pp. 353-378
-
-
Güntert, P.1
-
19
-
-
58849162221
-
Automated structure determination from NMR spectra
-
doi:10.1007/s00249-008-0367-z
-
protein PDB structures. J Biomol NMR 32(1):1-12. doi:10.1007/ s10858-005-2195-0Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38(2):129-143. doi:10.1007/s00249-008-0367-z
-
(2009)
Eur Biophys J
, vol.38
, Issue.2
, pp. 129-143
-
-
Güntert, P.1
-
20
-
-
4644223325
-
NOE assignment with ARIA 2.0: The nuts and bolts
-
doi:10.1385/1-59259-809-9:379
-
Habeck M, Rieping W, Linge JP, Nilges M (2004) NOE assignment with ARIA 2.0: The nuts and bolts. Methods Mol Biol (Clifton, NJ) 278:379-402. doi:10.1385/1-59259-809-9:379
-
(2004)
Methods Mol Biol (Clifton, NJ
, vol.278
, pp. 379-402
-
-
Habeck, M.1
Rieping, W.2
Linge, J.P.3
Nilges, M.4
-
21
-
-
77954298717
-
NMR constraints analyser: A webserver for the graphical analysis of NMR experimental constraints
-
(Web Server issue). doi:10.1093/nar/gkq484
-
Heller DM, Giorgetti A (2010) NMR constraints analyser: A webserver for the graphical analysis of NMR experimental constraints. Nucleic Acids Res 38(Web Server issue):W628-W632. doi:10.1093/nar/gkq484
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Heller, D.M.1
Giorgetti, A.2
-
22
-
-
38549176153
-
Remediation of the protein data bank archive
-
DOI 10.1093/nar/gkm937
-
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL et al (2008) Remediation of the protein data bank archive. Nucleic Acids Res 36(Database issue):D426-D433. doi:10.1093/nar/gkm937 (Pubitemid 351149761)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Henrick, K.1
Feng, Z.2
Bluhm, W.F.3
Dimitropoulos, D.4
Doreleijers, J.F.5
Dutta, S.6
Flippen-Anderson, J.L.7
Ionides, J.8
Kamada, C.9
Krissinel, E.10
Lawson, C.L.11
Markley, J.L.12
Nakamura, H.13
Newman, R.14
Shimizu, Y.15
Swaminathan, J.16
Velankar, S.17
Ory, J.18
Ulrich, E.L.19
Vranken, W.20
Westbrook, J.21
Yamashita, R.22
Yang, H.23
Young, J.24
Yousufuddin, M.25
Berman, H.M.26
more..
-
23
-
-
33746124556
-
Biomolecules in the computer: Jmol to the rescue
-
Herráez A (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 34(4):255-261
-
(2006)
Biochem Mol Biol Educ
, vol.34
, Issue.4
, pp. 255-261
-
-
Herráez, A.1
-
24
-
-
33646001409
-
Ca2? regulation in the Na?/ Ca2? exchanger involves two markedly different Ca2? sensors
-
doi101016/jmolcel2006.03008
-
Hilge M, Aelen JMA, VuisterGW(2006) Ca2? regulation in the Na?/ Ca2? exchanger involves two markedly different Ca2? sensors. Mol Cell 22(1):15-25. doi:10.1016/j.molcel.2006.03.008
-
(2006)
Mol Cell
, vol.22
, Issue.1
, pp. 15-25
-
-
Hilge, M.1
Aelen, J.M.A.2
Vuister, G.W.3
-
25
-
-
70149116358
-
Ca2? regulation in the Na?/Ca2? exchanger features a dual electrostatic switch mechanism
-
doi101073/nas0902171106
-
Hilge M, Aelen J, Foarce A, Perrakis A, Vuister GW (2009) Ca2? regulation in the Na?/Ca2? exchanger features a dual electrostatic switch mechanism. Proc Natl Acad Sci USA 106(34): 14333-14338. doi:10.1073/pnas.0902171106
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.34
, pp. 14333-14338
-
-
Hilge, M.1
Aelen, J.2
Foarce, A.3
Perrakis, A.4
Vuister, G.W.5
-
26
-
-
0030461976
-
The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value
-
Hooft RWW, Sander C, Scharf M, Vriend G (1996a) The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value. Bioinformatics 12(6):525-529. doi:10.1093/bioinformatics/12.6.525 (Pubitemid 27067446)
-
(1996)
Computer Applications in the Biosciences
, vol.12
, Issue.6
, pp. 525-529
-
-
Hooft, R.W.W.1
Sander, C.2
Scharf, M.3
Vriend, G.4
-
27
-
-
0030047142
-
Errors in protein structures
-
doi:10.1038/381272a0
-
Hooft R, Vriend G, Sander C, Abola E (1996b) Errors in protein structures. Nature 381(6580):272. doi:10.1038/381272a0
-
(1996)
Nature
, vol.381
, Issue.6580
, pp. 272
-
-
Hooft, R.1
Vriend, G.2
Sander, C.3
Abola, E.4
-
28
-
-
0030870075
-
Objectively judging the quality of a protein structure from a Ramachandran plot
-
Hooft RWW, Sander C, Vriend G (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Bioinformatics 13(4):425-430. doi:10.1093/bioinformatics/13. 4.425 (Pubitemid 27384626)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.4
, pp. 425-430
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
29
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
doi101109/MCSE2007.55
-
Hunter J (2007) Matplotlib: A 2D graphics environment. Comput Sci Eng 9(3):90-95. doi:10.1109/MCSE.2007.55
-
(2007)
Comput Sci Eng
, vol.9
, Issue.3
, pp. 90-95
-
-
Hunter, J.1
-
30
-
-
0018115846
-
Conformation of amino acid side chains in proteins
-
Janin J, Wodak S, Levitt M, Maigret B (1978) Conformation of amino acid side-chains in proteins. J Mol Biol 125(3):357-386. doi: 10.1016/0022-2836(78) 90408-4 (Pubitemid 9063908)
-
(1978)
Journal of Molecular Biology
, vol.125
, Issue.3
, pp. 357-386
-
-
Janin, J.1
Wodak, S.2
Levitt, M.3
Maigret, B.4
-
31
-
-
78651277458
-
A series of PDB related databases for everyday needs
-
doi:10.1093/nar/gkq1105
-
Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C et al (2011) A series of PDB related databases for everyday needs. Nucleic Acids Res 39:D411-D419. doi:10.1093/nar/gkq1105
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Joosten, R.P.1
Te Beek, T.A.H.2
Krieger, E.3
Hekkelman, M.L.4
Hooft, R.W.W.5
Schneider, R.6
Sander, C.7
-
32
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
doi101002/bi 360221211
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577-2637. doi:10.1002/bip. 360221211
-
(1983)
Biopolymers
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
33
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
DOI 10.1016/0263-7855(96)00009-4
-
Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graph 14(1):51-55. doi:10.1016/0263-7855(96)00009-4 (Pubitemid 26152976)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.1
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wuthrich, K.3
-
34
-
-
0036902235
-
Close-range electrostatic interactions in proteins
-
DOI 10.1002/1439-7633(200 20703)3:7<604::AID-CB IC604>3.0.CO;2-X
-
Kumar S, Nussinov R (2002) Close-range electrostatic interactions in proteins. Chembiochem: Eur J Chem Biol 3(7):604-617. doi: 10.1002/1439- 7633(20020703)3:7\604:AID-CBIC604[3.0.CO; 2-X (Pubitemid 36004524)
-
(2002)
ChemBioChem
, vol.3
, Issue.7
, pp. 604-617
-
-
Kumar, S.1
Nussinov, R.2
-
35
-
-
0037263939
-
Structural quality assurance
-
doi:10.1002/0471721204.ch14
-
Laskowski R (2003) Structural quality assurance. Methods Biochem Anal 44:273-303. doi:10.1002/0471721204.ch14
-
(2003)
Methods Biochem Anal
, vol.44
, pp. 273-303
-
-
Laskowski, R.1
-
36
-
-
0030339738
-
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
-
Laskowski R, Rullmann J, MacArthur M (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4):477-486. doi:10.1007/BF00228148 (Pubitemid 126706801)
-
(1996)
Journal of Biomolecular NMR
, vol.8
, Issue.4
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmann, J.A.C.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
-
37
-
-
23044509110
-
NMR data collection and analysis protocol for high-throughput protein structure determination
-
DOI 10.1073/pnas.0504338102
-
Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R et al (2005) NMR data collection and analysis protocol for highthroughput protein structure determination. Proc Natl Acad Sci USA 102(30):10487-10492. doi:10.1073/pnas.0504338102 (Pubitemid 41061581)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.30
, pp. 10487-10492
-
-
Liu, G.1
Shen, Y.2
Atreya, H.S.3
Parish, D.4
Shao, Y.5
Sukumaran, D.K.6
Xiao, R.7
Yee, A.8
Lemak, A.9
Bhattacharya, A.10
Acton, T.A.11
Arrowsmith, C.H.12
Montelione, G.T.13
Szyperski, T.14
-
38
-
-
0037441653
-
Structure validation by Ca geometry: φ, ξ and Cβ deviation
-
doi101002/rot10286
-
Lovell SC, Davis IW, Arendall WB III, de Bakker PIW, Word JM, Prisant MG, Richardson JS et al (2003) Structure validation by Ca geometry: φ, ξ and Cβ deviation. Proteins Struct Funct Bioinformatics 50(3):437-450. doi:10.1002/prot.10286
-
(2003)
Proteins Struct Funct Bioinformatics
, vol.50
, Issue.3
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
De Bakker, P.I.W.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
-
39
-
-
0003880237
-
-
2nd edn. O'Reilly, Sebastopol
-
Lutz M (2001) Programming python, 2nd edn. O'Reilly, Sebastopol
-
(2001)
Programming Python
-
-
Lutz, M.1
-
40
-
-
0032110340
-
Recommendations for the presentation of NMR structures of proteins and nucleic acids
-
Markley JL, Bax A, Arata Y, Hilbers C, Kaptein R, Sykes B, Wright P et al (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Biomol NMR 12(1):1-23
-
(1998)
J Biomol NMR
, vol.12
, Issue.1
, pp. 1-23
-
-
Markley, J.L.1
Bax, A.2
Arata, Y.3
Hilbers, C.4
Kaptein, R.5
Sykes, B.6
Wright, P.7
-
41
-
-
41149116500
-
Bio Mag Res Bank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions
-
doi101007/s10858-008-9221-y
-
Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) Bio Mag Res Bank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions. J Biomol NMR 40(3):153-155. doi:10.1007/s10858-008-9221-y
-
(2008)
J Biomol NMR
, vol.40
, Issue.3
, pp. 153-155
-
-
Markley, J.L.1
Ulrich, E.L.2
Berman, H.M.3
Henrick, K.4
Nakamura, H.5
Akutsu, H.6
-
42
-
-
35648988945
-
Benchmarking consensus model quality assessment for protein fold recognition
-
doi101186/1471-2105-8-345
-
McGuffin LJ (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics 8:345. doi:10.1186/1471-2105-8-345
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 345
-
-
McGuffin, L.J.1
-
43
-
-
79952591087
-
Python for scientists and engineers
-
doi:10.1109/MCSE.2011.36
-
Millman KJ, Aivazis M (2011) Python for scientists and engineers. Comput Sci Eng 13(2):9-12. doi:10.1109/MCSE.2011.36
-
(2011)
Comput Sci Eng
, vol.13
, Issue.2
, pp. 9-12
-
-
Millman, K.J.1
Aivazis, M.2
-
44
-
-
70349558318
-
Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts
-
doi101002/cbic200900086
-
Mulder F (2009) Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts. Chembiochem Eur J Chem Biol 10(9):1477-1479. doi:10.1002/cbic.200900086
-
(2009)
Chembiochem Eur J Chem Biol
, vol.10
, Issue.9
, pp. 1477-1479
-
-
Mulder, F.1
-
45
-
-
0141508959
-
Quantitative evaluation of experimental NMR restraints
-
DOI 10.1021/ja035440f
-
Nabuurs SB, Spronk CAEM, Krieger E, Maassen H, Vriend G, Vuister GW (2003) Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 125(39):12026-12034. doi: 10.1021/ja035440f (Pubitemid 37175433)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.39
, pp. 12026-12034
-
-
Nabuurs, S.B.1
Spronk, C.A.E.M.2
Krieger, E.3
Maassen, H.4
Vriend, G.5
Vuister, G.W.6
-
46
-
-
2442610955
-
DRESS: A database of refined solution NMR structures
-
DOI 10.1002/prot.20118
-
Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AMJJ, Vuister GW, Vriend G et al (2004) DRESS: A database of REfined solution NMR structures. Proteins Struct Funct Bioinformatics 55(3):483-486. doi:10.1002/prot.20118 (Pubitemid 38620072)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.3
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.J.J.5
Vuister, G.W.6
Vriend, G.7
Spronk, C.A.E.M.8
-
47
-
-
27944492860
-
Definition of a new information-based per-residue quality parameter
-
DOI 10.1007/s10858-005-2826-5
-
Nabuurs SB, Krieger E, Spronk CAEM, Nederveen AJ, Vriend G, Vuister GW (2005) Definition of a new information-based perresidue quality parameter. J Biomol NMR 33(2):123-134. doi: 10.1007/s10858-005-2826-5 (Pubitemid 41662434)
-
(2005)
Journal of Biomolecular NMR
, vol.33
, Issue.2
, pp. 123-134
-
-
Nabuurs, S.B.1
Krieger, E.2
Spronk, C.A.E.M.3
Nederveen, A.J.4
Vriend, G.5
Vuister, G.W.6
-
48
-
-
33645790319
-
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
-
doi: 10.1371/journal.pcbi.0020009
-
Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2(2):e9. doi: 10.1371/journal.pcbi.0020009
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.2
-
-
Nabuurs, S.B.1
Caem, S.2
Vuister, G.W.3
Vriend, G.4
-
49
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
DOI 10.1002/prot.20408
-
Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P et al (2005) RECOORD: A recalculated coordinate database of 500? proteins from the PDB using restraints from the Bio Mag Res Bank. Proteins Struct Funct Bioinformatics 59(4):662-672. doi:10.1002/prot.20408 (Pubitemid 40695843)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.E.M.5
Nabuurs, S.B.6
Guntert, P.7
Livny, M.8
Markley, J.L.9
Nilges, M.10
Ulrich, E.L.11
Kaptein, R.12
Bonvin, A.M.J.J.13
-
50
-
-
45949117843
-
A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data
-
doi:10.1016/0014-5793(87)81181-X
-
Nilges M, Clore G, Gronenborn A (1987) A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data. FEBS Lett 219(1):11-16. doi:10.1016/0014-5793(87) 81181-X
-
(1987)
FEBS Lett
, vol.219
, Issue.1
, pp. 11-16
-
-
Nilges, M.1
Clore, G.2
Gronenborn, A.3
-
51
-
-
33748282179
-
Multi-template approach to modeling engineered bisulfide bonds
-
DOI 10.1002/prot.21059
-
Pellequer J-L, Chen S-WW (2006) Multi-template approach to modeling engineered disulfide bonds. Proteins Struct Funct Bioinformatics 65(1):192-202. doi:10.1002/(ISSN)1097-0134 (Pubitemid 44320628)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.1
, pp. 192-202
-
-
Pellequer, J.-L.1
Chen, S.-W.W.2
-
52
-
-
77955794370
-
Validation of archived chemical shifts through atomic coordinates
-
doi:10.1002/prot.22756
-
Rieping W, Vranken WF (2010) Validation of archived chemical shifts through atomic coordinates. Proteins Struct Funct Bioinformatics 78(11):2482-2489. doi:10.1002/prot.22756
-
(2010)
Proteins Struct Funct Bioinformatics
, vol.78
, Issue.11
, pp. 2482-2489
-
-
Rieping, W.1
Vranken, W.F.2
-
53
-
-
33847283016
-
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
-
DOI 10.1093/bioinformatics/btl589
-
Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M (2007) ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23(3):381-382. doi:10.1093/bioinformatics/btl589 (Pubitemid 46323164)
-
(2007)
Bioinformatics
, vol.23
, Issue.3
, pp. 381-382
-
-
Rieping, W.1
Bardiaux, B.2
Bernard, A.3
Malliavin, T.E.4
Nilges, M.5
-
54
-
-
69549138143
-
CASD-NMR: Critical assessment of automated structure determination by NMR
-
doi101038/nmeth0909-625-626 doi101038/nmeth0625
-
Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A et al (2009) CASD-NMR: Critical assessment of automated structure determination by NMR. Nat Methods 6(9):625-626. doi:10.1038/nmeth0909-625
-
(2009)
Nat Methods
, vol.6
, Issue.9
, pp. 625-626
-
-
Rosato, A.1
Bagaria, A.2
Baker, D.3
Bardiaux, B.4
Cavalli, A.5
Doreleijers, J.F.6
Giachetti, A.7
-
55
-
-
84863011912
-
Blind testing of routine, fully automated determination of protein structures from NMR data
-
doi:10.1016/j.str.2012.01.002
-
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF et al (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20(2):227-236. doi:10.1016/j.str.2012.01.002
-
(2012)
Structure
, vol.20
, Issue.2
, pp. 227-236
-
-
Rosato, A.1
Aramini, J.M.2
Arrowsmith, C.3
Bagaria, A.4
Baker, D.5
Cavalli, A.6
Doreleijers, J.F.7
-
56
-
-
41349112195
-
Peirce's criterion for the elimination of suspect experimental data
-
Ross S (2003) Peirce's criterion for the elimination of suspect experimental data. J Eng Technol 20(2):38-41
-
(2003)
J Eng Technol
, vol.20
, Issue.2
, pp. 38-41
-
-
Ross, S.1
-
57
-
-
84868207659
-
Using Xplor-NIH for NMR molecular structure determination
-
doi101002/chin200644278
-
Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. ChemInform 37(44):47-62. doi:10.1002/chin. 200644278
-
(2006)
ChemInform
, vol.37
, Issue.44
, pp. 47-62
-
-
Schwieters, C.D.1
Kuszewski, J.J.2
Clore, G.M.3
-
58
-
-
77951666856
-
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
-
doi:10.1007/s10858-009-9395-y
-
Shen Y, Bax A (2009) Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts. J Biomol NMR 46(3):199-204. doi:10.1007/s10858- 009-9395-y
-
(2009)
J Biomol NMR
, vol.46
, Issue.3
, pp. 199-204
-
-
Shen, Y.1
Bax, A.2
-
59
-
-
42449146665
-
Consistent blind protein structure generation from NMR chemical shift data
-
DOI 10.1073/pnas.0800256105
-
Shen Y, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Lemak A et al (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105(12):4685-4690. doi:10.1073/pnas.0800256105 (Pubitemid 351753807)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.12
, pp. 4685-4690
-
-
Shen, Y.1
Lange, O.2
Delaglio, F.3
Rossi, P.4
Aramini, J.M.5
Liu, G.6
Eletsky, A.7
Wu, Y.8
Singarapu, K.K.9
Lemak, A.10
Ignatchenko, A.11
Arrowsmith, C.H.12
Szyperski, T.13
Montelione, G.T.14
Baker, D.15
Bax, A.16
-
60
-
-
68349093958
-
TALOS?: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
-
doi: 10.1007/s10858-009-9333-z
-
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS?: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44(4):213-223. doi: 10.1007/s10858-009-9333-z
-
(2009)
J Biomol NMR
, vol.44
, Issue.4
, pp. 213-223
-
-
Shen, Y.1
Delaglio, F.2
Cornilescu, G.3
Bax, A.4
-
61
-
-
18844415920
-
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
-
DOI 10.1002/prot.20402
-
Snyder D, Montelione G (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins Struct 59(4):673-686. doi:10.1002/prot. 20402 (Pubitemid 40695844)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 673-686
-
-
Snyder, D.A.1
Montelione, G.T.2
-
62
-
-
18844433630
-
Assessing precision and accuracy of protein structures derived from NMR data
-
DOI 10.1002/prot.20499
-
Snyder DA, Bhattacharya A, Huang YJ, Montelione GT (2005) Assessing precision and accuracy of protein structures derived from NMR data. Proteins Struct Funct Bioinformatics 59(4):655-661. doi:10.1002/prot.20499 (Pubitemid 40695842)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 655-661
-
-
Snyder, D.A.1
Bhattacharya, A.2
Huang, Y.J.3
Montelione, G.T.4
-
63
-
-
28144455335
-
Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex
-
DOI 10.1016/j.jmb.2005.10.017, PII S0022283605012507
-
Song J, Tyler RC, Lee MS, Tyler EM, Markley JL (2005) Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex. J Mol Biol 354(5):1043-1051. doi:10.1016/ j.jmb.2005.10.017 (Pubitemid 41698914)
-
(2005)
Journal of Molecular Biology
, vol.354
, Issue.5
, pp. 1043-1051
-
-
Song, J.1
Tyler, R.C.2
Lee, M.S.3
Tyler, E.M.4
Markley, J.L.5
-
64
-
-
0036219167
-
Improving the quality of protein structures derived by NMR spectroscopy
-
DOI 10.1023/A:1014971029663
-
Spronk CAEM, Linge JP, Hilbers CW, Vuister GW (2002) Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 22(3):281-289 (Pubitemid 34296110)
-
(2002)
Journal of Biomolecular NMR
, vol.22
, Issue.3
, pp. 281-289
-
-
Spronk, C.A.E.M.1
Linge, J.P.2
Hilbers, C.W.3
Vuister, G.W.4
-
65
-
-
19444382397
-
The CCPN data model for NMR spectroscopy: Development of a software pipeline
-
DOI 10.1002/prot.20449
-
Vranken W, Boucher W, Stevens T, Fogh R, Pajon A, Llinas M, Ulrich EL et al (2005) The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins Struct Funct Bioinformatics 59:687-696. doi:10.1002/prot. 20449 (Pubitemid 40695845)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 687-696
-
-
Vranken, W.F.1
Boucher, W.2
Stevens, T.J.3
Fogh, R.H.4
Pajon, A.5
Llinas, M.6
Ulrich, E.L.7
Markley, J.L.8
Ionides, J.9
Laue, E.D.10
-
66
-
-
77952661254
-
Importance Of The C-terminal Loop L137-S141 for the folding and folding stability of staphylococcal nuclease
-
doi:10.1021/bi100118k
-
Wang M, Feng Y, Yao H, Wang J (2010) Importance of the C-terminal loop L137-S141 for the folding and folding stability of staphylococcal nuclease. Biochemistry 49(20):4318-4326. doi:10.1021/bi100118k
-
(2010)
Biochemistry
, vol.49
, Issue.20
, pp. 4318-4326
-
-
Wang, M.1
Feng, Y.2
Yao, H.3
Wang, J.4
-
67
-
-
84877009732
-
WeNMR structural biology on the grid
-
urn:nbn:de:0074-819-5
-
Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, Jaravine V, Güntert P, Schwalbe H, Vranken WF, Doreleijers JF, Vriend G, Vuister GW, Franke D, Kikhney A, Svergun DI, Fogh R, Ionides J, Laue ED, Spronk CAE, Verlato A, Badoer S, Dal Pra S, Mazzucato M, Frizziero E, Bonvin AMJJ (2011) WeNMR: Structural biology on the grid. IWSG proceedings, urn:nbn:de:0074-819-5
-
(2011)
IWSG Proceedings
-
-
Wassenaar, T.A.1
Van Dijk, M.2
Loureiro-Ferreira, N.3
Van Der Schot, G.4
De Vries, S.J.5
Schmitz, C.6
Van Der Zwan, J.7
Boelens, R.8
Giachetti, A.9
Ferella, L.10
Rosato, A.11
Bertini, I.12
Herrmann, T.13
Jonker, H.R.A.14
Bagaria, A.15
Jaravine, V.16
Güntert, P.17
Schwalbe, H.18
Vranken, W.F.19
Doreleijers, J.F.20
Vriend, G.21
Vuister, G.W.22
Franke, D.23
Kikhney, A.24
Svergun, D.I.25
Fogh, R.26
Ionides, J.27
Laue, E.D.28
Spronk, C.A.E.29
Verlato, A.30
Badoer, S.31
Dal Pra, S.32
Mazzucato, M.33
Frizziero, E.34
Amjj, B.35
more..
-
68
-
-
0039299578
-
Who checks the checkers? Four validation tools applied to eight atomic resolution structures
-
DOI 10.1006/jmbi.1997.1526
-
Wilson K, Dauter Z, Lamzin V, Walsh M, Wodak S, Richelle J, Pontius J et al (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J Mol Biol 276:417-436. doi:10.1006/jmbi.1997.1526 (Pubitemid 28085330)
-
(1998)
Journal of Molecular Biology
, vol.276
, Issue.2
, pp. 417-436
-
-
Wilson, K.S.1
Butterworth, S.2
Dauter, Z.3
Lamzin, V.S.4
Walsh, M.5
Wodak, S.6
Pontius, J.7
Richelle, J.8
Vaguine, A.9
Sander, C.10
Hooft, R.W.W.11
Vriend, G.12
Thornton, J.M.13
Laskowski, R.A.14
MacArthur, M.W.15
Dodson, E.J.16
Murshudov, G.17
Oldfield, T.J.18
Kaptein, R.19
Rullmann, J.A.C.20
more..
-
69
-
-
0037354231
-
RefDB: A database of uniformly referenced protein chemical shifts
-
DOI 10.1023/A:1022836027055
-
Zhang H, Neal S, Wishart DS (2003) RefDB: A database of uniformly referenced protein chemical shifts. J Biomol NMR 25(3):173-195. doi:10.1023/A:1022836027055 (Pubitemid 36410583)
-
(2003)
Journal of Biomolecular NMR
, vol.25
, Issue.3
, pp. 173-195
-
-
Zhang, H.1
Neal, S.2
Wishart, D.S.3
|