메뉴 건너뛰기




Volumn 3, Issue 4, 2000, Pages 408-422

The role of macromolecular crystallography and structure for drug discovery: Advances and caveats

Author keywords

Crystallographic refinement; Macromolecular crystallography; Molecular modeling; Structure based drug design

Indexed keywords

ARTICLE; CRYSTALLOGRAPHY; DRUG DESIGN; DRUG STRUCTURE; MOLECULAR MODEL; X RAY CRYSTALLOGRAPHY;

EID: 0033910487     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (13)

References (82)
  • 1
    • 0031856212 scopus 로고    scopus 로고
    • The second decade - Into the third millennium
    • 492-495.
    • Wuthrich K: The second decade - into the third millennium. Nature Struct B/o/(1998) (Suppl):492-495.
    • (1998) Nature Struct B/o/ , Issue.SUPPL.
    • Wuthrich, K.1
  • 2
    • 0042624145 scopus 로고    scopus 로고
    • Comparative proteins structure modeling in genomics
    • Sali A: 388-401.
    • Sanchez R, Sali A: Comparative proteins structure modeling in genomics. J Comp Phys (1999) 151:388-401.
    • (1999) J Comp Phys , vol.151
    • Sanchez, R.1
  • 3
    • 0032876705 scopus 로고    scopus 로고
    • CASP3 comparative modeling evaluation
    • Kleywegt GJ: Suppl 3: 30-46. A concise overview of the recent CASP3 results in comparative modeling.
    • Jones TA, Kleywegt GJ: CASP3 comparative modeling evaluation. Proteins (1999) 37 (Suppl 3):30-46. A concise overview of the recent CASP3 results in comparative modeling.
    • (1999) Proteins , vol.37
    • Jones, T.A.1
  • 4
    • 0030791762 scopus 로고    scopus 로고
    • X-ray crystallography and NMR reveal complementary views of structure and dynamics
    • 862-865. An excellent analysis of the relative precision and, by extension, accuracies of crystallography and NMR.
    • Brunger AT: X-ray crystallography and NMR reveal complementary views of structure and dynamics. Nature Struct Biol (1997) 4:862-865. An excellent analysis of the relative precision (and, by extension, accuracies) of crystallography and NMR.
    • (1997) Nature Struct Biol , vol.4
    • Brunger, A.T.1
  • 5
    • 0032606076 scopus 로고    scopus 로고
    • Some measures of comparative performance in the three CASPs
    • Zemla A, Fidelis K, Moult J: 231-237. An examination of the advancement of modeling techniques over the three CASP meetings.
    • Venclovas C, Zemla A, Fidelis K, Moult J: Some measures of comparative performance in the three CASPs. Proteins (1999) (Suppl 3):231-237. An examination of the advancement of modeling techniques over the three CASP meetings.
    • (1999) Proteins , vol.3
    • Venclovas, C.1
  • 6
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Hajduk PJ, Meadows RP, Fesik SW: 1531-1534.
    • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW: Discovering high-affinity ligands for proteins: SAR by NMR. Science (1996)274:1531-1534.
    • (1996) Science , vol.274
    • Shuker, S.B.1
  • 7
    • 0032900490 scopus 로고    scopus 로고
    • NMR screening in drug discovery
    • 54-58.
    • Moore JM: NMR screening in drug discovery. Curr Opin Biotechnol (1999) 10:54-58.
    • (1999) Curr Opin Biotechnol , vol.10
    • Moore, J.M.1
  • 8
    • 85070027549 scopus 로고    scopus 로고
    • Crystallization of Biological Macromolecules
    • NY, USA
    • McPherson A (Ed): Crystallization of Biological Macromolecules. Cold Spring Harbor Press, NY, USA (1999).
    • (1999) Cold Spring Harbor Press
  • 10
    • 0028584269 scopus 로고
    • Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
    • Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR: 1981-1986.
    • Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR: Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases. Science (1994) 266:1981-1986.
    • (1994) Science , vol.266
    • Dyda, F.1
  • 11
    • 0030767713 scopus 로고    scopus 로고
    • Free R value: Cross-validation in crystallography
    • 366-396. An informative overview of the free R-factor value and of the concept of cross-validation in crystallography.
    • Brunger AT: Free R value: Cross-validation in crystallography. Methods Enzymol (1997) 277:366-396. An informative overview of the free R-factor value and of the concept of cross-validation in crystallography.
    • (1997) Methods Enzymol , vol.277
    • Brunger, A.T.1
  • 12
    • 0032881809 scopus 로고    scopus 로고
    • X-ray crystal structures of 70S ribosome functional complexes
    • Yusupov MM, Yusupova GZ, Earnest TN, Noller HF: 2095-2104. Describes the crystal structure of 70S ribosomal complexes from a bacterium, which is an extremely large structure.
    • Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF: X-ray crystal structures of 70S ribosome functional complexes. Science (1999) 285:2095-2104. Describes the crystal structure of 70S ribosomal complexes from a bacterium, which is an extremely large structure.
    • (1999) Science , vol.285
    • Cate, J.H.1
  • 13
    • 0033607003 scopus 로고    scopus 로고
    • Placement of protein and RNA structures into a 5 a resolution map of the SOS ribosomal subunit
    • Nissen P, Hansen J, Capel M, Moore PB, Steitz TA: 841-847. Describes the crystal structure of the SOS ribosomal subunit from a bacterium, which is an extremely large structure.
    • Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA: Placement of protein and RNA structures into a 5 A resolution map of the SOS ribosomal subunit. Nature (1999) 400:841-847. Describes the crystal structure of the SOS ribosomal subunit from a bacterium, which is an extremely large structure.
    • (1999) Nature , vol.400
    • Ban, N.1
  • 14
    • 0344809971 scopus 로고    scopus 로고
    • Structure of a bacterial 30S ribosomal subunit at 5.5 a resolution
    • May JL, Wimberty BT, McCutcheon JP, Capel MS, Ramakrishnan V: 833-840. Describes the crystal structure of the 305 ribosomal subunit from a bacterial thermophile, which is an extremely large structure.
    • demons WM Jr, May JL, Wimberty BT, McCutcheon JP, Capel MS, Ramakrishnan V: Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature (1999) 400:833-840. Describes the crystal structure of the 305 ribosomal subunit from a bacterial thermophile, which is an extremely large structure.
    • (1999) Nature , vol.400
    • May Jr., W.M.1
  • 15
    • 0033213587 scopus 로고    scopus 로고
    • Experiences with CCD detectors on a home X-ray source
    • 1669-1671. A comparison of CCD detectors to image plate systems.
    • Muchmore SW: Experiences with CCD detectors on a home X-ray source. Acta Crystallogr D Biol Crystallogr (1999) 55:1669-1671. A comparison of CCD detectors to image plate systems.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Muchmore, S.W.1
  • 16
    • 0033213486 scopus 로고    scopus 로고
    • Macromolecular crystallography with a third-generation synchrotron source. An introduction to a third generation synchrotron source.
    • Lindley PR Macromolecular crystallography with a third-generation synchrotron source. Acta Crystallogr D Biol Crystallogr (1999) 55:1654-1662. An introduction to a third generation synchrotron source.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55 , pp. 1654-1662
    • Lindley, P.R.1
  • 18
    • 85070034307 scopus 로고    scopus 로고
    • Practical Protein Crystallography
    • CA, USA
    • McRee DL (Ed): Practical Protein Crystallography. Academic Press, CA, USA (1999).
    • (1999) Academic Press
    • McRee, D.L.1
  • 20
    • 0032942076 scopus 로고    scopus 로고
    • Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement. Acta Crystallogr D Biol Crystallogr (1999) 55:181-190
    • Pannu NS, Read RJ, Brunger AT
    • Adams PA, Pannu NS, Read RJ, Brunger AT: Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement. Acta Crystallogr D Biol Crystallogr (1999) 55:181-190. An outline of the molecular replacement algorithm implemented in CNS.
    • An Outline of the Molecular Replacement Algorithm Implemented in CNS.
    • Adams, P.A.1
  • 21
    • 0033081529 scopus 로고    scopus 로고
    • Rapid automated molecular replacement by evolutionary search
    • Gehlhaar DK, Fogel DB: 484-491.
    • Kissinger CR, Gehlhaar DK, Fogel DB: Rapid automated molecular replacement by evolutionary search. Acta Crystallogr D Biol Crystallogr (1999) 55:484-491.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Kissinger, C.R.1
  • 22
    • 0032214097 scopus 로고    scopus 로고
    • HAD, a data bank of heavy-atom binding sites in protein crystals: A resource for use in multiple isomorphous replacement and anomalous scattering
    • Carvin D, Stemberg MJ, Blundell TL: 1199-1206.
    • Islam SA, Carvin D, Stemberg MJ, Blundell TL: HAD, a data bank of heavy-atom binding sites in protein crystals: A resource for use in multiple isomorphous replacement and anomalous scattering. Acta Crystallogr D Biol Crystallogr (1998)54:1199-1206.
    • (1998) Acta Crystallogr D Biol Crystallogr , vol.54
    • Islam, S.A.1
  • 23
    • 0031903288 scopus 로고    scopus 로고
    • MAD phasing grows up
    • S638-S640.
    • Ogata CM: MAD phasing grows up. Nature Struct Biol (1998) 5:S638-S640.
    • (1998) Nature Struct Biol , vol.5
    • Ogata, C.M.1
  • 24
    • 0033213109 scopus 로고    scopus 로고
    • MAD data collection - Current trends
    • Evans G, Sanishvili R, Dementieva I, Joachimiak A: 1726-1732. Describes the latest in MAD data collection and structure determination.
    • Walsh MA, Evans G, Sanishvili R, Dementieva I, Joachimiak A: MAD data collection - current trends. Acta Crystallogr D Biol Crystallogr (1999) 55:1726-1732. Describes the latest in MAD data collection and structure determination.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Walsh, M.A.1
  • 25
    • 0033119895 scopus 로고    scopus 로고
    • Automated MAD and MIR structure solution
    • Berendzen J: 849-861.
    • Terwilliger TC, Berendzen J: Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr (1999) 55:849-861.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Terwilliger, T.C.1
  • 26
    • 0032986806 scopus 로고    scopus 로고
    • Sigma2R
    • a reciprocal-space measure of the quality of macromolecular electron-density maps. 1174-1178.
    • Terwilliger TC: Sigma2R, a reciprocal-space measure of the quality of macromolecular electron-density maps. Acta Crystallogr D Biol Crystallogr (1999) 55:1174-1178.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Terwilliger, T.C.1
  • 27
    • 0033229885 scopus 로고    scopus 로고
    • Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density
    • Berendzen J: 1872-1877.
    • Terwilliger TC, Berendzen J: Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density. Acta Crystallogr D Biol Crystallogr (1999) 55:1872-1877.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Terwilliger, T.C.1
  • 28
    • 0033082065 scopus 로고    scopus 로고
    • Optimizing Shake-and-Bake for proteins
    • Miller R: 492-500.
    • Weeks CM, Miller R: Optimizing Shake-and-Bake for proteins. Acta Crystallogr D Biol Crystallogr (1999) 55:492-500.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Weeks, C.M.1
  • 29
    • 0030783379 scopus 로고    scopus 로고
    • Phasing methods for protein crystallography
    • 672-680.
    • Hauptman H: Phasing methods for protein crystallography. Curr Opin Struct Biol (1997) 7:672-680.
    • (1997) Curr Opin Struct Biol , vol.7
    • Hauptman, H.1
  • 30
    • 0022325950 scopus 로고
    • Resolution of phase ambiguity in macromolecular crystallography
    • 90-112.
    • Wang BC: Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymo/(1985) 115:90-112.
    • (1985) Methods Enzymo/ , vol.115
    • Wang, B.C.1
  • 32
    • 0033229975 scopus 로고    scopus 로고
    • Experimental assessment of differences between related protein crystal structures
    • 1878-1884.
    • Kleywegt GJ: Experimental assessment of differences between related protein crystal structures. Acta Crystallogr D Biol Crystallogr(1999) 55:1878-1884.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Kleywegt, G.J.1
  • 33
    • 0030863952 scopus 로고    scopus 로고
    • Noncrystallographic symmetry averaging in phase refinement and extension
    • Read RJ: 18-53. An in-depth review of the use of non-crystallographic symmetry in crystallography.
    • Vellieux FM, Read RJ: Noncrystallographic symmetry averaging in phase refinement and extension. Methods £hzymo/(1997) 277:18-53. An in-depth review of the use of non-crystallographic symmetry in crystallography.
    • (1997) Methods £Hzymo/ , vol.277
    • Vellieux, F.M.1
  • 34
    • 0017295828 scopus 로고
    • Automated interpretation of electron density maps of proteins: Derivation of atomic coordinates for the main chain
    • 427-458.
    • Gréer J: Automated interpretation of electron density maps of proteins: Derivation of atomic coordinates for the main chain. J Mol Biol (1976) 100:427-458.
    • (1976) J Mol Biol , vol.100
    • Gréer, J.1
  • 35
    • 0032806795 scopus 로고    scopus 로고
    • A database method for automated map interpretation in protein crystallography
    • Redinbo MR, Pohl E, Hol WG: 526-541.
    • Diller DJ, Redinbo MR, Pohl E, Hol WG: A database method for automated map interpretation in protein crystallography. Proteins (1999) 36:526-541.
    • (1999) Proteins , vol.36
    • Diller, D.J.1
  • 37
    • 0031937561 scopus 로고    scopus 로고
    • Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP
    • Perrakis A, Kalk KH, Lamzin VS, Dijkstra BW: 58-73.
    • Van Asselt EJ, Perrakis A, Kalk KH, Lamzin VS, Dijkstra BW: Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP. Acta Crystallogr D Biol Crystallogr (1998) 54:58-73.
    • (1998) Acta Crystallogr D Biol Crystallogr , vol.54
    • Van Asselt, E.J.1
  • 38
    • 0030845843 scopus 로고    scopus 로고
    • Model building and refinement practice
    • Jones TA: 208-230. A review of the building of the initial atomic model and its subsequent refinement.
    • Kleywegt GJ, Jones TA: Model building and refinement practice. Methods Enzymol (1997) 277:208-230. A review of the building of the initial atomic model and its subsequent refinement.
    • (1997) Methods Enzymol , vol.277
    • Kleywegt, G.J.1
  • 39
    • 0030841587 scopus 로고    scopus 로고
    • Electron-density map Interpretation
    • Kjelgaard M: 173-208. An excellent review of the map interpretation process.
    • Jones TA, Kjelgaard M: Electron-density map Interpretation. Metf70CfeEnzymo/(1997) 1997:173-208. An excellent review of the map interpretation process.
    • (1997) Metf70CfeEnzymo/ , vol.1997
    • Jones, T.A.1
  • 40
    • 0344541116 scopus 로고    scopus 로고
    • Recent developments for the efficient crystallographic refinement of macromolecular structures
    • Adams PD, Rice LM: 606-611. An excellent review of current refinement protocols and advancements.
    • Brunger AT, Adams PD, Rice LM: Recent developments for the efficient crystallographic refinement of macromolecular structures. Curr Opin Struct Biol (1998) 8:606-611. An excellent review of current refinement protocols and advancements.
    • (1998) Curr Opin Struct Biol , vol.8
    • Brunger, A.T.1
  • 41
    • 0032847732 scopus 로고    scopus 로고
    • Annealing in crystallography: A powerful optimization tool
    • Adams PD, Rice LM: 135-155.
    • Brunger AT, Adams PD, Rice LM: Annealing in crystallography: A powerful optimization tool. Prog Biophys Wo/β/o/(1999) 72:135-155.
    • (1999) Prog Biophys Wo/β/o/ , vol.72
    • Brunger, A.T.1
  • 43
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Bowie JU, Eisenberg D: 83-85. A protein model validation method, which relies on protein-folding rules.
    • Luthy R, Bowie JU, Eisenberg D: Assessment of protein models with three-dimensional profiles. Nature (1992) 356:83-85. A protein model validation method, which relies on protein-folding rules.
    • (1992) Nature , vol.356
    • Luthy, R.1
  • 44
    • 0039299578 scopus 로고    scopus 로고
    • D validation network: Who checks the checkers? Four validation tools applied to eight atomic resolution structures
    • Butterworth S, Dauter Z, Lamzin VS, Walsh M, Wodak S, Pontius J, Richelle J, Vaguine A, Sander C, Hooft RW, Vriend G, Thomton JM, Laskowski RA, MacArthur MW, Dodson EJ, Murshudov G, Oldfield TJ, Kaptein R, Rullmann JA: 3- 417-436. An in-depth evaluation of several validation tools.
    • Wilson KS, Butterworth S, Dauter Z, Lamzin VS, Walsh M, Wodak S, Pontius J, Richelle J, Vaguine A, Sander C, Hooft RW, Vriend G, Thomton JM, Laskowski RA, MacArthur MW, Dodson EJ, Murshudov G, Oldfield TJ, Kaptein R, Rullmann JA: 3-D validation network: Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J Mol Biol (1998) 276:417-436. An in-depth evaluation of several validation tools.
    • (1998) J Mol Biol , vol.276
    • Wilson, K.S.1
  • 45
    • 0032896079 scopus 로고    scopus 로고
    • Difference density quality (DDQ): A method to assess the global and local correctness of macromolecular crystal structures
    • Hol WG: 206-218. A structure validation method that validates a structure's correctness based on responses to perturbations within various types of electron-density maps.
    • van den Akker F, Hol WG: Difference density quality (DDQ): A method to assess the global and local correctness of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr (1999) 55:206-218. A structure validation method that validates a structure's correctness based on responses to perturbations within various types of electron-density maps.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55
    • Akker, F.1
  • 46
    • 0034013435 scopus 로고    scopus 로고
    • Validation of protein crystal structures
    • 249-265. An excellent review of protein structure validation methods.
    • Kleywegt GJ: Validation of protein crystal structures. Acta Crystallogr D Biol Crystallogr (2000) 56:249-265. An excellent review of protein structure validation methods.
    • (2000) Acta Crystallogr D Biol Crystallogr , vol.56
    • Kleywegt, G.J.1
  • 47
    • 0033613812 scopus 로고    scopus 로고
    • Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
    • Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC: 1711-1733. An interesting paper examining the slight mispositioning caused by not representing the hydrogen atoms during refinement.
    • Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC: Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms. J Mol Biol (1999)285:1711-1733. An interesting paper examining the slight mispositioning caused by not representing the hydrogen atoms during refinement.
    • (1999) J Mol Biol , vol.285
    • Word, J.M.1
  • 48
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side chain amide orientation
    • Lovell SC, Richardson JS, Richardson DC: 1735-1747.
    • Word JM, Lovell SC, Richardson JS, Richardson DC: Asparagine and glutamine: Using hydrogen atom contacts in the choice of side chain amide orientation. J Mol Biol (1999) 285:1735-1747.
    • (1999) J Mol Biol , vol.285
    • Word, J.M.1
  • 49
    • 0032918978 scopus 로고    scopus 로고
    • Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure
    • Oikonomakos NG, Zographos SE, Skamnaki VT, Gregoriou M, Watson KA, Johnson LN, Fleet GW: 741-749. This paper examines the insidious effects of additives in a crystallization experiment.
    • Tsitsanou KE, Oikonomakos NG, Zographos SE, Skamnaki VT, Gregoriou M, Watson KA, Johnson LN, Fleet GW: Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure. Protein Sci (1999) 8:741-749. This paper examines the insidious effects of additives in a crystallization experiment.
    • (1999) Protein Sci , vol.8
    • Tsitsanou, K.E.1
  • 50
    • 0034097788 scopus 로고    scopus 로고
    • Sructural characterization of protein-denaturant interactions: Crystal structures of hen egg-white lysozyme in complex with DMSO and guanidinium chloride
    • Sobhia ME: 13:133-141. An examination of the structural effects of a common additive to crystallization buffers, ie, DMSO.
    • Mande SC, Sobhia ME: Sructural characterization of protein-denaturant interactions: Crystal structures of hen egg-white lysozyme in complex with DMSO and guanidinium chloride. Protein Eng(2QQQ) 13:133-141. An examination of the structural effects of a common additive to crystallization buffers, ie, DMSO.
    • Protein Eng , vol.2
    • Mande, S.C.1
  • 51
    • 0028037899 scopus 로고
    • Human rhinovirus 14 complexed with fragments of active antiviral compounds
    • Kremer MJ, Rossmann MG, Diana GD, Dutko FJ, Pevear DC, McKinlay MA: 360-369. Another example of DMSO binding to a protein.
    • Bibler-Muckelbauer JK, Kremer MJ, Rossmann MG, Diana GD, Dutko FJ, Pevear DC, McKinlay MA: Human rhinovirus 14 complexed with fragments of active antiviral compounds. Virology (1994) 202:360-369. Another example of DMSO binding to a protein.
    • (1994) Virology , vol.202
    • Bibler-Muckelbauer, J.K.1
  • 52
    • 0033607028 scopus 로고    scopus 로고
    • Structure-based identification of small molecule antiviral compounds targeted to the gp41 core structure of the human immunodeficiency virus type 1
    • Radigan L, Jiang S: 3203-3209.
    • Debnath AK, Radigan L, Jiang S: Structure-based identification of small molecule antiviral compounds targeted to the gp41 core structure of the human immunodeficiency virus type 1. J Med Chem (1999) 42:3203-3209.
    • (1999) J Med Chem , vol.42
    • Debnath, A.K.1
  • 53
    • 6244283606 scopus 로고    scopus 로고
    • Critical evaluation of search algorithms for automated molecular docking and database screening
    • Kuntz ID: 1175-1189. A recent advance on the DOCK program from UCSF, which remains the most widely-used and widely-tested docking-screening program.
    • Ewing TJ, Kuntz ID: Critical evaluation of search algorithms for automated molecular docking and database screening. JComput C/7em(1997) 18:1175-1189. A recent advance on the DOCK program from UCSF, which remains the most widely-used and widely-tested docking-screening program.
    • (1997) JComput C/7em , vol.18
    • Ewing, T.J.1
  • 54
    • 0032190489 scopus 로고    scopus 로고
    • Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
    • Swanson CA, Getzoff ED, Tainer JA, Kühn LA: 74-87.
    • Schnecke V, Swanson CA, Getzoff ED, Tainer JA, Kühn LA: Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins (1998) 33:74-87.
    • (1998) Proteins , vol.33
    • Schnecke, V.1
  • 55
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
    • Rarey M, Lengauer T: 228-241. A test of the ability of FlexX to reproduce a large number of protein-ligand complexes from the PDB. FlexX is a popular and widely available docking program.
    • Kramer B, Rarey M, Lengauer T: Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins (1999) 37:228-241. A test of the ability of FlexX to reproduce a large number of protein-ligand complexes from the PDB. FlexX is a popular and widely available docking program.
    • (1999) Proteins , vol.37
    • Kramer, B.1
  • 56
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Shoichet BK: 938-950.
    • Lorber DM, Shoichet BK: Flexible ligand docking using conformational ensembles. Protein Sci (1998) 7:938-950.
    • (1998) Protein Sci , vol.7
    • Lorber, D.M.1
  • 57
    • 13344275187 scopus 로고    scopus 로고
    • Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase
    • Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Oison A, Duncan B, Rao M, Jackson R, Stemberg M, James MN: 233-239. The crystallography group of Michael James challenged six docking groups to predict the structure of a protein-protein complex before its structure had been determined. All six groups successfully predicted the overall structure of the complex, although some key polar interactions were missed.
    • Strynadka MC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Oison A, Duncan B, Rao M, Jackson R, Stemberg M, James MN: Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nature Struct β/o/(1996) 3:233-239. The crystallography group of Michael James challenged six docking groups to predict the structure of a protein-protein complex before its structure had been determined. All six groups successfully predicted the overall structure of the complex, although some key polar interactions were missed.
    • (1996) Nature Struct β/O/ , vol.3
    • Strynadka, M.C.1
  • 58
    • 0031297617 scopus 로고    scopus 로고
    • Critical evaluation of the Research docking program for the CASP2 challenge
    • Ness SR, Read RJ: 205-209. A report on the success of the Research docking program in a recent CASP test of computational methods. This program was one of the more successful of the programs tested. Broadly, the docking methods did well, though they were by no means able to predict all complexes.
    • Hart TN, Ness SR, Read RJ: Critical evaluation of the Research docking program for the CASP2 challenge. Proteins (1997) (Suppl 1):205-209. A report on the success of the Research docking program in a recent CASP test of computational methods. This program was one of the more successful of the programs tested. Broadly, the docking methods did well, though they were by no means able to predict all complexes.
    • (1997) Proteins , vol.1
    • Hart, T.N.1
  • 59
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Goodsell DS, Huey R, Oison AJ: 293-304. An update of the AutoDock program, which is widely used to predict the structures of single complexes.
    • Morris GM, Goodsell DS, Huey R, Oison AJ: Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J Comput Aided Mol Des (1996)10:293-304. An update of the AutoDock program, which is widely used to predict the structures of single complexes.
    • (1996) J Comput Aided Mol Des , vol.10
    • Morris, G.M.1
  • 60
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Leach AR, Kuntz ID: 4-16. Explicit ligand desolvation penalties are introduced into a derivative of DOCK. To get sensible rankings in molecular docking, it is critical to include desolvation energies in one form or another. This remains an area of active investigation.
    • Shoichet BK, Leach AR, Kuntz ID: Ligand solvation in molecular docking. Proteins (1999) 34:4-16. Explicit ligand desolvation penalties are introduced into a derivative of DOCK. To get sensible rankings in molecular docking, it is critical to include desolvation energies in one form or another. This remains an area of active investigation.
    • (1999) Proteins , vol.34
    • Shoichet, B.K.1
  • 61
    • 0033214412 scopus 로고    scopus 로고
    • Exhaustive docking of molecular fragments with electrostatic solvation
    • Scarsi M, Apostolakis J, Ehrhardt C, Caflisch A: 88-105.
    • Majeux N, Scarsi M, Apostolakis J, Ehrhardt C, Caflisch A: Exhaustive docking of molecular fragments with electrostatic solvation. Proteins (1999) 37:88-105.
    • (1999) Proteins , vol.37
    • Majeux, N.1
  • 62
    • 0033536456 scopus 로고    scopus 로고
    • Inclusion of solvation in ligand binding free energy calculations using the generalizedborn model
    • Sun Y, Kuntz ID: 8033-8043.
    • Zou X, Sun Y, Kuntz ID: Inclusion of solvation in ligand binding free energy calculations using the generalizedborn model. JAm Chem Soc(1999) 121:8033-8043.
    • (1999) JAm Chem Soc , vol.121
    • Zou, X.1
  • 63
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Martin YC: 791-804.
    • Muegge I, Martin YC: A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J Med Chem (1999) 42:791-804.
    • (1999) J Med Chem , vol.42
    • Muegge, I.1
  • 64
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Corkery JJ, Murcko MA, Walters WP: 5100-5109. This paper presents a side-by-side comparison of many popular docking scoring methods against experimental data collected by the Vertex group.
    • Charifson PS, Corkery JJ, Murcko MA, Walters WP: Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem (1999) 42:5100-5109. This paper presents a side-by-side comparison of many popular docking scoring methods against experimental data collected by the Vertex group.
    • (1999) J Med Chem , vol.42
    • Charifson, P.S.1
  • 65
    • 0032708785 scopus 로고    scopus 로고
    • Efficacy and selectivity in flexible database docking
    • Wagener M: 334-345.
    • Knegtel RM, Wagener M: Efficacy and selectivity in flexible database docking. Proteins (1999) 37:334-345.
    • (1999) Proteins , vol.37
    • Knegtel, R.M.1
  • 67
    • 0027480452 scopus 로고
    • Structure-based inhibitor design by using protein models for the development of antiparasitic agents
    • Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE: 3583-3587.
    • Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE: Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc NatlAcadSci USA (1993) 90:3583-3587.
    • (1993) Proc NatlAcadSci USA , vol.90
    • Ring, C.S.1
  • 68
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • Baxter CA, Frenkel AD: 547-562.
    • Murray CW, Baxter CA, Frenkel AD: The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des (1999) 13:547-562.
    • (1999) J Comput Aided Mol Des , vol.13
    • Murray, C.W.1
  • 69
    • 0027522358 scopus 로고
    • Structure-based discovery of inhibitors of thymidylate synthase
    • Stroud RM, Santi DV, Kuntz ID, Perry KM: 1445-1450.
    • Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM: Structure-based discovery of inhibitors of thymidylate synthase. Science (1993) 259:1445-1450.
    • (1993) Science , vol.259
    • Shoichet, B.K.1
  • 72
    • 0029643784 scopus 로고    scopus 로고
    • The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 a resolution: Implications for a new mode of inhibition
    • Stroud RM: 67-77.
    • Stout TJ, Stroud RM: The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: Implications for a new mode of inhibition. Structure (1996) 4:67-77.
    • (1996) Structure , vol.4
    • Stout, T.J.1
  • 73
    • 0025054246 scopus 로고
    • Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease
    • Scibel GL, Kuntz ID, Furth PS, Alvarez JC, Ortiz de Montellano PR, DeCamp DL, Babe LM, Craik CS: 6644-6648.
    • DesJarlais RL, Scibel GL, Kuntz ID, Furth PS, Alvarez JC, Ortiz de Montellano PR, DeCamp DL, Babe LM, Craik CS: Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. P roc Natl Acad Sci USA (1990) 87:6644-6648.
    • (1990) P Roc Natl Acad Sci USA , vol.87
    • Desjarlais, R.L.1
  • 74
    • 0032554638 scopus 로고    scopus 로고
    • Rational design of novel antimicrobials: Blocking purine salvage in a parasitic protozoan
    • Skillman AG Jr, Munagala NR, Oshiro CM, Knegtel RM, Mpoke S, Fletterick RJ, Kuntz ID, Wang CC: 5344-5348.
    • Somoza JR, Skillman AG Jr, Munagala NR, Oshiro CM, Knegtel RM, Mpoke S, Fletterick RJ, Kuntz ID, Wang CC: Rational design of novel antimicrobials: Blocking purine salvage in a parasitic protozoan. Biochemistry (1998) 37:5344-5348.
    • (1998) Biochemistry , vol.37
    • Somoza, J.R.1
  • 75
    • 13144295022 scopus 로고    scopus 로고
    • Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-β-lactamase
    • Fitzgerald PM, Grover-Sharma N, Oison SH, May WJ, Sundelof JG, Vanderwall DE, Cleary KA, Grant SK, Wu JK, Kozarich JW, Pompliano DL, Hammond GG: 185-196.
    • Toney JH, Fitzgerald PM, Grover-Sharma N, Oison SH, May WJ, Sundelof JG, Vanderwall DE, Cleary KA, Grant SK, Wu JK, Kozarich JW, Pompliano DL, Hammond GG: Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-β-lactamase. Chem Biol (1998)5:185-196.
    • (1998) Chem Biol , vol.5
    • Toney, J.H.1
  • 76
    • 0027523625 scopus 로고
    • Inhibition of the fusion-Inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones
    • Yamasaki RB, Buswell RL, Steams JF, White JM, Kuntz ID: 2967-2978.
    • Bodian DL, Yamasaki RB, Buswell RL, Steams JF, White JM, Kuntz ID: Inhibition of the fusion-Inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones. Biochemistry (1993) 32:2967-2978.
    • (1993) Biochemistry , vol.32
    • Bodian, D.L.1
  • 77
    • 0034646180 scopus 로고    scopus 로고
    • Inhibitors of kinesin activity from structure-based computer screening
    • Vale RD, Kuntz ID: 2805-2814.
    • Hopkins SC, Vale RD, Kuntz ID: Inhibitors of kinesin activity from structure-based computer screening. Biochemistry (2000)39:2805-2814.
    • (2000) Biochemistry , vol.39
    • Hopkins, S.C.1
  • 78
    • 0030753409 scopus 로고    scopus 로고
    • Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: Irreversible inhibition of infectivity
    • Kuntz ID, White JM: 8808-8820.
    • Hotfman LR, Kuntz ID, White JM: Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: Irreversible inhibition of infectivity. J V/ro/(1997) 71:8808-8820.
    • (1997) J V/ro/ , vol.71
    • Hotfman, L.R.1
  • 79
    • 0034719423 scopus 로고    scopus 로고
    • Structure-based discovery of small molecule inhibitors targeted to protein tyrosine phosphatase 1 B
    • Wu L, Keng YF, Song L, Luo Z, Huang 2, Wu GZ, Yuan AK, Zhang ZY: 146-155.
    • Sarmiento M, Wu L, Keng YF, Song L, Luo Z, Huang 2, Wu GZ, Yuan AK, Zhang ZY: Structure-based discovery of small molecule inhibitors targeted to protein tyrosine phosphatase 1 B. J Med Chem (2000) 43:146-155.
    • (2000) J Med Chem , vol.43
    • Sarmiento, M.1
  • 80
    • 0034628541 scopus 로고    scopus 로고
    • Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads
    • Xu K, Kollmeyer TM, Kaufmann SH, Prendergast FG, Pang YP: 401-408.
    • Perola E, Xu K, Kollmeyer TM, Kaufmann SH, Prendergast FG, Pang YP: Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads. J Med Chem (2000) 43:401-408.
    • (2000) J Med Chem , vol.43
    • Perola, E.1
  • 81
    • 0030964552 scopus 로고    scopus 로고
    • Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase
    • Sirawarapom W, Santi DV, Kuntz ID: 29:59-67.
    • Gschwend DA, Sirawarapom W, Santi DV, Kuntz ID: Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase. Proteins CQ97) 29:59-67.
    • Proteins CQ , vol.97
    • Gschwend, D.A.1
  • 82
    • 0033965389 scopus 로고    scopus 로고
    • Rational discovery of novel nuclear hormone receptor antagonists
    • Raaka BM, Samuels HH, Abagyan R: 1008-1013.
    • Schapira M, Raaka BM, Samuels HH, Abagyan R: Rational discovery of novel nuclear hormone receptor antagonists. Proc Natl Acad Sci USA (2000) 97:1008-1013.
    • (2000) Proc Natl Acad Sci USA , vol.97
    • Schapira, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.