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Volumn 57, Issue 10, 2017, Pages 2437-2447

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; ELECTRON DENSITY MEASUREMENT; ELECTRONS; LATTICE CONSTANTS; MACROMOLECULES; STRUCTURAL DESIGN; X RAYS;

EID: 85032011007     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.7b00391     Document Type: Article
Times cited : (61)

References (69)
  • 1
    • 37349016530 scopus 로고    scopus 로고
    • Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures
    • Wlodawer, A.; Minor, W.; Dauter, Z.; Jaskolski, M. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures FEBS J. 2008, 275, 1-21 10.1111/j.1742-4658.2007.06178.x
    • (2008) FEBS J. , vol.275 , pp. 1-21
    • Wlodawer, A.1    Minor, W.2    Dauter, Z.3    Jaskolski, M.4
  • 2
    • 0038336897 scopus 로고    scopus 로고
    • Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
    • Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design Angew. Chem., Int. Ed. 2003, 42, 2718-2736 10.1002/anie.200200539
    • (2003) Angew. Chem., Int. Ed. , vol.42 , pp. 2718-2736
    • Davis, A.M.1    Teague, S.J.2    Kleywegt, G.J.3
  • 3
    • 80054078285 scopus 로고    scopus 로고
    • A New Generation of Crystallographic Validation Tools for the Protein Data Bank
    • Read, R. et al. A New Generation of Crystallographic Validation Tools for the Protein Data Bank Structure 2011, 19, 1395-1412 10.1016/j.str.2011.08.006
    • (2011) Structure , vol.19 , pp. 1395-1412
    • Read, R.1
  • 4
    • 84944353843 scopus 로고    scopus 로고
    • Models of protein-ligand crystal structures: Trust, but verify
    • Deller, M. C.; Rupp, B. Models of protein-ligand crystal structures: trust, but verify J. Comput.-Aided Mol. Des. 2015, 29, 817-836 10.1007/s10822-015-9833-8
    • (2015) J. Comput.-Aided Mol. Des. , vol.29 , pp. 817-836
    • Deller, M.C.1    Rupp, B.2
  • 9
    • 84922531078 scopus 로고    scopus 로고
    • BDB: Databank of PDB files with consistent B-factors
    • Touw, W. G.; Vriend, G. BDB: databank of PDB files with consistent B-factors Protein Eng., Des. Sel. 2014, 27, 457-462 10.1093/protein/gzu044
    • (2014) Protein Eng., Des. Sel. , vol.27 , pp. 457-462
    • Touw, W.G.1    Vriend, G.2
  • 14
    • 85032009366 scopus 로고    scopus 로고
    • Molecular Operating Environment (MOE). (January 14, 2016)
    • Molecular Operating Environment (MOE). http://www.chemcomp.com (January 14, 2016).
  • 15
    • 50249136103 scopus 로고    scopus 로고
    • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
    • Langer, G.; Cohen, S. X.; Lamzin, V. S.; Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protoc. 2008, 3, 1171-1179 10.1038/nprot.2008.91
    • (2008) Nat. Protoc. , vol.3 , pp. 1171-1179
    • Langer, G.1    Cohen, S.X.2    Lamzin, V.S.3    Perrakis, A.4
  • 16
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, 47, 110-119 10.1107/S0108767390010224
    • (1991) Acta Crystallogr., Sect. A: Found. Crystallogr. , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 17
    • 84860305929 scopus 로고    scopus 로고
    • Statistical quality indicators for electron-density maps
    • Tickle, I. J. Statistical quality indicators for electron-density maps Acta Crystallogr., Sect. D: Biol. Crystallogr. 2012, 68, 454-467 10.1107/S0907444911035918
    • (2012) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.68 , pp. 454-467
    • Tickle, I.J.1
  • 18
    • 0030841587 scopus 로고    scopus 로고
    • Electron Density Map Interpretation
    • Jones, T.; Kjeldgaard, M. Electron Density Map Interpretation Methods Enzymol. 1997, 277, 173-208 10.1016/S0076-6879(97)77012-5
    • (1997) Methods Enzymol. , vol.277 , pp. 173-208
    • Jones, T.1    Kjeldgaard, M.2
  • 19
    • 49449086848 scopus 로고    scopus 로고
    • An alternative method for the evaluation of docking performance: RSR vs RMSD
    • Yusuf, D.; Davis, A. M.; Kleywegt, G. J.; Schmitt, S. An alternative method for the evaluation of docking performance: RSR vs RMSD J. Chem. Inf. Model. 2008, 48, 1411-1422 10.1021/ci800084x
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1411-1422
    • Yusuf, D.1    Davis, A.M.2    Kleywegt, G.J.3    Schmitt, S.4
  • 21
    • 84870308957 scopus 로고    scopus 로고
    • Essential considerations for using protein-ligand structures in drug discovery
    • Warren, G. L.; Do, T. D.; Kelley, B. P.; Nicholls, A.; Warren, S. D. Essential considerations for using protein-ligand structures in drug discovery Drug Discovery Today 2012, 17, 1270-1281 10.1016/j.drudis.2012.06.011
    • (2012) Drug Discovery Today , vol.17 , pp. 1270-1281
    • Warren, G.L.1    Do, T.D.2    Kelley, B.P.3    Nicholls, A.4    Warren, S.D.5
  • 23
    • 84903302003 scopus 로고    scopus 로고
    • Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
    • Li, Y.; Liu, Z.; Li, J.; Han, L.; Liu, J.; Zhao, Z.; Wang, R. Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set J. Chem. Inf. Model. 2014, 54, 1700-1716 10.1021/ci500080q
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1700-1716
    • Li, Y.1    Liu, Z.2    Li, J.3    Han, L.4    Liu, J.5    Zhao, Z.6    Wang, R.7
  • 25
    • 84928689662 scopus 로고    scopus 로고
    • Evidence of water molecules - A statistical evaluation of water molecules based on electron density
    • Nittinger, E.; Schneider, N.; Lange, G.; Rarey, M. Evidence of water molecules-a statistical evaluation of water molecules based on electron density J. Chem. Inf. Model. 2015, 55, 771-783 10.1021/ci500662d
    • (2015) J. Chem. Inf. Model. , vol.55 , pp. 771-783
    • Nittinger, E.1    Schneider, N.2    Lange, G.3    Rarey, M.4
  • 26
    • 84891774970 scopus 로고    scopus 로고
    • PDBe: Protein Data Bank in Europe
    • Gutmanas, A. et al. PDBe: Protein Data Bank in Europe Nucleic Acids Res. 2014, 42, D285-D291 10.1093/nar/gkt1180
    • (2014) Nucleic Acids Res. , vol.42 , pp. D285-D291
    • Gutmanas, A.1
  • 27
  • 29
    • 67650410033 scopus 로고    scopus 로고
    • Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase
    • Jeudy, S.; Lartigue, A.; Claverie, J.-M.; Abergel, C. Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase J. Virol. 2009, 83, 7142-7150 10.1128/JVI.00511-09
    • (2009) J. Virol. , vol.83 , pp. 7142-7150
    • Jeudy, S.1    Lartigue, A.2    Claverie, J.-M.3    Abergel, C.4
  • 30
    • 84903286855 scopus 로고    scopus 로고
    • Facing the challenges of structure-based target prediction by inverse virtual screening
    • Schomburg, K. T.; Bietz, S.; Briem, H.; Henzler, A. M.; Urbaczek, S.; Rarey, M. Facing the challenges of structure-based target prediction by inverse virtual screening J. Chem. Inf. Model. 2014, 54, 1676-1686 10.1021/ci500130e
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1676-1686
    • Schomburg, K.T.1    Bietz, S.2    Briem, H.3    Henzler, A.M.4    Urbaczek, S.5    Rarey, M.6
  • 32
    • 85032004029 scopus 로고    scopus 로고
    • Crystal structure of 3-HSA hydroxylase, oxygenase from Rhodococcus sp. RHA1
    • DOI
    • Chang, C.; Skarina, T.; Kagan, O.; Savchenko, A.; Edwards, A.; Joachimiak, A. Crystal structure of 3-HSA hydroxylase, oxygenase from Rhodococcus sp. RHA1. PDB 2007; DOI: 10.2210/pdb2rfq/pdb.
    • (2007) PDB
    • Chang, C.1    Skarina, T.2    Kagan, O.3    Savchenko, A.4    Edwards, A.5    Joachimiak, A.6
  • 34
    • 80053920610 scopus 로고    scopus 로고
    • Dihydroquinazolines as a novel class of Trypanosoma brucei trypanothione reductase inhibitors: Discovery, synthesis, and characterization of their binding mode by protein crystallography
    • Patterson, S.; Alphey, M. S.; Jones, D. C.; Shanks, E. J.; Street, I. P.; Frearson, J. A.; Wyatt, P. G.; Gilbert, I. H.; Fairlamb, A. H. Dihydroquinazolines as a novel class of Trypanosoma brucei trypanothione reductase inhibitors: Discovery, synthesis, and characterization of their binding mode by protein crystallography J. Med. Chem. 2011, 54, 6514-6530 10.1021/jm200312v
    • (2011) J. Med. Chem. , vol.54 , pp. 6514-6530
    • Patterson, S.1    Alphey, M.S.2    Jones, D.C.3    Shanks, E.J.4    Street, I.P.5    Frearson, J.A.6    Wyatt, P.G.7    Gilbert, I.H.8    Fairlamb, A.H.9
  • 35
    • 84899877851 scopus 로고    scopus 로고
    • Crystallographic and Glycan Microarray Analysis of Human Polyomavirus 9 VP1 Identifies N-Glycolyl Neuraminic Acid as a Receptor Candidate
    • Khan, Z. M.; Liu, Y.; Neu, U.; Gilbert, M.; Ehlers, B.; Feizi, T.; Stehle, T. Crystallographic and Glycan Microarray Analysis of Human Polyomavirus 9 VP1 Identifies N-Glycolyl Neuraminic Acid as a Receptor Candidate J. Virol. 2014, 88, 6100-6111 10.1128/JVI.03455-13
    • (2014) J. Virol. , vol.88 , pp. 6100-6111
    • Khan, Z.M.1    Liu, Y.2    Neu, U.3    Gilbert, M.4    Ehlers, B.5    Feizi, T.6    Stehle, T.7
  • 36
    • 84868089459 scopus 로고    scopus 로고
    • Conformational changes in orotidine 5′-monophosphate decarboxylase: A structure-based explanation for how the 5-phosphate group activates the enzyme
    • Desai, B. J.; Wood, B. M. K.; Fedorov, A. A.; Fedorov, E. V.; Goryanova, B.; Amyes, T. L.; Richard, J. P.; Almo, S. C.; Gerlt, J. A. Conformational changes in orotidine 5′-monophosphate decarboxylase: A structure-based explanation for how the 5-phosphate group activates the enzyme Biochemistry 2012, 51, 8665-8678 10.1021/bi301188k
    • (2012) Biochemistry , vol.51 , pp. 8665-8678
    • Desai, B.J.1    Wood, B.M.K.2    Fedorov, A.A.3    Fedorov, E.V.4    Goryanova, B.5    Amyes, T.L.6    Richard, J.P.7    Almo, S.C.8    Gerlt, J.A.9
  • 37
    • 0345735668 scopus 로고    scopus 로고
    • The 2.0 Å Resolution Crystal Structure of Prostaglandin H 2 Synthase-1: Structural Insights into an Unusual Peroxidase
    • Gupta, K.; Selinsky, B. S.; Kaub, C. J.; Katz, A. K.; Loll, P. J. The 2.0 Å Resolution Crystal Structure of Prostaglandin H 2 Synthase-1: Structural Insights into an Unusual Peroxidase J. Mol. Biol. 2004, 335, 503-518 10.1016/j.jmb.2003.10.073
    • (2004) J. Mol. Biol. , vol.335 , pp. 503-518
    • Gupta, K.1    Selinsky, B.S.2    Kaub, C.J.3    Katz, A.K.4    Loll, P.J.5
  • 38
    • 0345269288 scopus 로고    scopus 로고
    • Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis
    • Brenk, R.; Naerum, L.; Grädler, U.; Gerber, H. D.; Garcia, G. A.; Reuter, K.; Stubbs, M. T.; Klebe, G. Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis J. Med. Chem. 2003, 46, 1133-1143 10.1021/jm0209937
    • (2003) J. Med. Chem. , vol.46 , pp. 1133-1143
    • Brenk, R.1    Naerum, L.2    Grädler, U.3    Gerber, H.D.4    Garcia, G.A.5    Reuter, K.6    Stubbs, M.T.7    Klebe, G.8
  • 40
    • 0035965124 scopus 로고    scopus 로고
    • Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors
    • Ren, J.; Nichols, C.; Bird, L.; Chamberlain, P.; Weaver, K.; Short, S.; Stuart, D. I.; Stammers, D. K. Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors J. Mol. Biol. 2001, 312, 795-805 10.1006/jmbi.2001.4988
    • (2001) J. Mol. Biol. , vol.312 , pp. 795-805
    • Ren, J.1    Nichols, C.2    Bird, L.3    Chamberlain, P.4    Weaver, K.5    Short, S.6    Stuart, D.I.7    Stammers, D.K.8
  • 41
    • 84969528711 scopus 로고    scopus 로고
    • Structures of C-mannosylated anti-adhesives bound to the type 1 fimbrial FimH adhesin
    • De Ruyck, J.; Lensink, M. F.; Bouckaert, J. Structures of C-mannosylated anti-adhesives bound to the type 1 fimbrial FimH adhesin IUCrJ 2016, 3, 163-167 10.1107/S2052252516002487
    • (2016) IUCrJ , vol.3 , pp. 163-167
    • De Ruyck, J.1    Lensink, M.F.2    Bouckaert, J.3
  • 42
    • 84896696883 scopus 로고    scopus 로고
    • Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza a virus
    • Tsurumura, T.; Qiu, H.; Yoshida, T.; Tsumori, Y.; Hatakeyama, D.; Kuzuhara, T.; Tsuge, H. Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza a virus PLoS One 2013, 8, e82020 10.1371/journal.pone.0082020
    • (2013) PLoS One , vol.8 , pp. e82020
    • Tsurumura, T.1    Qiu, H.2    Yoshida, T.3    Tsumori, Y.4    Hatakeyama, D.5    Kuzuhara, T.6    Tsuge, H.7
  • 44
    • 84934987870 scopus 로고    scopus 로고
    • Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations
    • Yu, L.; Lee, S.-J.; Yee, V. C. Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations Biochemistry 2015, 54, 3640-3648 10.1021/acs.biochem.5b00425
    • (2015) Biochemistry , vol.54 , pp. 3640-3648
    • Yu, L.1    Lee, S.-J.2    Yee, V.C.3
  • 47
    • 34248187243 scopus 로고    scopus 로고
    • The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10°C
    • Ohishi, H.; Tozuka, Y.; Da-Yang, Z.; Ishida, T.; Nakatani, K. The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10°C Biochem. Biophys. Res. Commun. 2007, 358, 24-28 10.1016/j.bbrc.2007.04.026
    • (2007) Biochem. Biophys. Res. Commun. , vol.358 , pp. 24-28
    • Ohishi, H.1    Tozuka, Y.2    Da-Yang, Z.3    Ishida, T.4    Nakatani, K.5
  • 48
    • 74449084306 scopus 로고    scopus 로고
    • Detailed assessment of X-ray induced structural perturbation in a crystalline state protein
    • Takeda, K.; Kusumoto, K.; Hirano, Y.; Miki, K. Detailed assessment of X-ray induced structural perturbation in a crystalline state protein J. Struct. Biol. 2010, 169, 135-144 10.1016/j.jsb.2009.09.012
    • (2010) J. Struct. Biol. , vol.169 , pp. 135-144
    • Takeda, K.1    Kusumoto, K.2    Hirano, Y.3    Miki, K.4
  • 49
    • 0030498233 scopus 로고    scopus 로고
    • XdlMAPMAN and xdlDATAMAN - Programs for Reformatting, Analysis and Manipulation of Biomacromolecular Electron-Density Maps and Reflection Data Sets
    • Kleywegt, G. J.; Jones, T. A. xdlMAPMAN and xdlDATAMAN-Programs for Reformatting, Analysis and Manipulation of Biomacromolecular Electron-Density Maps and Reflection Data Sets Acta Crystallogr., Sect. D: Biol. Crystallogr. 1996, 52, 826-828 10.1107/S0907444995014983
    • (1996) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.52 , pp. 826-828
    • Kleywegt, G.J.1    Jones, T.A.2
  • 50
    • 6344226669 scopus 로고    scopus 로고
    • Crystal structures of the phosphorylated and unphosphorylated kinase domains of the Cdc42-associated tyrosine kinase ACK1
    • Lougheed, J. C.; Chen, R. H.; Mak, P.; Stout, T. J. Crystal structures of the phosphorylated and unphosphorylated kinase domains of the Cdc42-associated tyrosine kinase ACK1 J. Biol. Chem. 2004, 279, 44039-44045 10.1074/jbc.M406703200
    • (2004) J. Biol. Chem. , vol.279 , pp. 44039-44045
    • Lougheed, J.C.1    Chen, R.H.2    Mak, P.3    Stout, T.J.4
  • 51
    • 0035808599 scopus 로고    scopus 로고
    • Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors
    • Davis, S. T. et al. Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors Science 2001, 291, 134-137 10.1126/science.291.5501.134
    • (2001) Science , vol.291 , pp. 134-137
    • Davis, S.T.1
  • 52
    • 20844442458 scopus 로고    scopus 로고
    • Structural basis for the activity of drugs that inhibit phosphodiesterases
    • Card, G. L. et al. Structural basis for the activity of drugs that inhibit phosphodiesterases Structure 2004, 12, 2233-2247 10.1016/j.str.2004.10.004
    • (2004) Structure , vol.12 , pp. 2233-2247
    • Card, G.L.1
  • 53
    • 0347927707 scopus 로고    scopus 로고
    • Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Crystallographic studies
    • Blaszczyk, J.; Li, Y.; Shi, G.; Yan, H.; Ji, X. Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Crystallographic studies Biochemistry 2003, 42, 1573-1580 10.1021/bi0267994
    • (2003) Biochemistry , vol.42 , pp. 1573-1580
    • Blaszczyk, J.1    Li, Y.2    Shi, G.3    Yan, H.4    Ji, X.5
  • 54
    • 0031054817 scopus 로고    scopus 로고
    • Protein Eng. with monomeric triosephosphate isomerase (monoTIM): The modelling and structure verification of a seven-residue loop
    • Thanki, N.; Zeelen, J. P.; Mathieu, M.; Jaenicke, R.; Abagyan, R. A.; Wierenga, R. K.; Schliebs, W. Protein Eng. with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop Protein Eng., Des. Sel. 1997, 10, 159-167 10.1093/protein/10.2.159
    • (1997) Protein Eng., Des. Sel. , vol.10 , pp. 159-167
    • Thanki, N.1    Zeelen, J.P.2    Mathieu, M.3    Jaenicke, R.4    Abagyan, R.A.5    Wierenga, R.K.6    Schliebs, W.7
  • 55
    • 0033524008 scopus 로고    scopus 로고
    • Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants
    • Hopkins, A. L.; Ren, J.; Tanaka, H.; Baba, M.; Okamato, M.; Stuart, D. I.; Stammers, D. K. Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants J. Med. Chem. 1999, 42, 4500-4505 10.1021/jm990192c
    • (1999) J. Med. Chem. , vol.42 , pp. 4500-4505
    • Hopkins, A.L.1    Ren, J.2    Tanaka, H.3    Baba, M.4    Okamato, M.5    Stuart, D.I.6    Stammers, D.K.7
  • 56
    • 0034650342 scopus 로고    scopus 로고
    • Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents
    • Liu, S.; Neidhardt, E. A.; Grossman, T. H.; Ocain, T.; Clardy, J. Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents Structure 2000, 8, 25-33 10.1016/S0969-2126(00)00077-0
    • (2000) Structure , vol.8 , pp. 25-33
    • Liu, S.1    Neidhardt, E.A.2    Grossman, T.H.3    Ocain, T.4    Clardy, J.5
  • 57
    • 0026799307 scopus 로고
    • Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: Analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography
    • Sauter, N. K.; Hanson, J. E.; Glick, G. D.; Brown, J. H.; Crowther, R. L.; Park, S. J.; Skehel, J. J.; Wiley, D. C. Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography Biochemistry 1992, 31, 9609-96021 10.1021/bi00155a013
    • (1992) Biochemistry , vol.31 , pp. 9609-96021
    • Sauter, N.K.1    Hanson, J.E.2    Glick, G.D.3    Brown, J.H.4    Crowther, R.L.5    Park, S.J.6    Skehel, J.J.7    Wiley, D.C.8
  • 58
    • 84883209345 scopus 로고    scopus 로고
    • CSAR benchmark exercise 2011-2012: Evaluation of results from docking and relative ranking of blinded congeneric series
    • Damm-Ganamet, K. L.; Smith, R. D.; Dunbar, J. B.; Stuckey, J. A.; Carlson, H. A. CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series J. Chem. Inf. Model. 2013, 53, 1853-1870 10.1021/ci400025f
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 1853-1870
    • Damm-Ganamet, K.L.1    Smith, R.D.2    Dunbar, J.B.3    Stuckey, J.A.4    Carlson, H.A.5
  • 59
    • 84901610512 scopus 로고    scopus 로고
    • The application of statistical methods to cognate docking: A path forward?
    • Hawkins, P. C. D.; Kelley, B. P.; Warren, G. L. The application of statistical methods to cognate docking: A path forward? J. Chem. Inf. Model. 2014, 54, 1339-1355 10.1021/ci5001086
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1339-1355
    • Hawkins, P.C.D.1    Kelley, B.P.2    Warren, G.L.3
  • 60
    • 85032007393 scopus 로고
    • Refined Crystal Structure of the Mc/Pc603 Fab-Phosphocholine Complex at 3.1 Angstroms Resolution
    • DOI
    • Padlan, E.; Cohen, G.; Davies, D. Refined Crystal Structure of the Mc/Pc603 Fab-Phosphocholine Complex at 3.1 Angstroms Resolution. PDB 1984; DOI: 10.2210/pdb2mcp/pdb.
    • (1984) PDB
    • Padlan, E.1    Cohen, G.2    Davies, D.3
  • 62
    • 21744434413 scopus 로고    scopus 로고
    • Crystal Structure of the Double Complex of the Tyrosine Sensitive Dahp Synthase from Yeast
    • DOI
    • Koenig, V.; Pfeil, A.; Heinrich, G.; Braus, G.; Schneider, T. Crystal Structure of the Double Complex of the Tyrosine Sensitive Dahp Synthase from Yeast. PDB 2004; DOI: 10.2210/pdb1of6/pdb.
    • (2004) PDB
    • Koenig, V.1    Pfeil, A.2    Heinrich, G.3    Braus, G.4    Schneider, T.5
  • 63
    • 21244496076 scopus 로고    scopus 로고
    • Structure-based design of novel Chk1 inhibitors: Insights into hydrogen bonding and protein-ligand affinity
    • Foloppe, N.; Fisher, L. M.; Howes, R.; Kierstan, P.; Potter, A.; Robertson, A. G. S.; Surgenor, A. E. Structure-based design of novel Chk1 inhibitors: Insights into hydrogen bonding and protein-ligand affinity J. Med. Chem. 2005, 48, 4332-4345 10.1021/jm049022c
    • (2005) J. Med. Chem. , vol.48 , pp. 4332-4345
    • Foloppe, N.1    Fisher, L.M.2    Howes, R.3    Kierstan, P.4    Potter, A.5    Robertson, A.G.S.6    Surgenor, A.E.7
  • 64
    • 0034718568 scopus 로고    scopus 로고
    • Detailed Structural Analysis of Glycosidase/Inhibitor Interactions: Complexes of Cex from Cellulomonas fimi with Xylobiose-Derived Aza-Sugars
    • Notenboom, V.; Williams, S. J.; Hoos, R.; Withers, S. G.; Rose, D. R. Detailed Structural Analysis of Glycosidase/Inhibitor Interactions: Complexes of Cex from Cellulomonas fimi with Xylobiose-Derived Aza-Sugars Biochemistry 2000, 39, 11553-11563 10.1021/bi0010625
    • (2000) Biochemistry , vol.39 , pp. 11553-11563
    • Notenboom, V.1    Williams, S.J.2    Hoos, R.3    Withers, S.G.4    Rose, D.R.5
  • 65
    • 85025095555 scopus 로고    scopus 로고
    • High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators
    • Friedrich, N.-O.; Meyder, A.; de Bruyn Kops, C.; Sommer, K.; Flachsenberg, F.; Rarey, M.; Kirchmair, J. High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators J. Chem. Inf. Model. 2017, 57, 529-539 10.1021/acs.jcim.6b00613
    • (2017) J. Chem. Inf. Model. , vol.57 , pp. 529-539
    • Friedrich, N.-O.1    Meyder, A.2    De Bruyn Kops, C.3    Sommer, K.4    Flachsenberg, F.5    Rarey, M.6    Kirchmair, J.7
  • 67
    • 34247481878 scopus 로고    scopus 로고
    • IPython: A system for interactive scientific computing
    • Pérez, F.; Granger, B. E. IPython: A system for interactive scientific computing Comput. Sci. Eng. 2007, 9, 21-29 10.1109/MCSE.2007.53
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 21-29
    • Pérez, F.1    Granger, B.E.2
  • 68
    • 0004062749 scopus 로고    scopus 로고
    • Wolfram Research Inc. Version 9.0
    • Wolfram Research Inc. Mathematica, Version 9.0; 2012.
    • (2012) Mathematica


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.