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Volumn 48, Issue 6, 2008, Pages 1257-1268

Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; BINDING ENERGY; DIAGNOSIS; LIGANDS; PROTEINS; RNA;

EID: 47349127321     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci8000327     Document Type: Article
Times cited : (90)

References (68)
  • 1
    • 0141676629 scopus 로고    scopus 로고
    • The process of structure-based drug design
    • Anderson, A. C. The process of structure-based drug design. Chem. Biol. 2003, 10, 787-97.
    • (2003) Chem. Biol , vol.10 , pp. 787-797
    • Anderson, A.C.1
  • 3
    • 34547093657 scopus 로고    scopus 로고
    • Aminoglycoside antibiotics: Old drugs and new therapeutic approaches
    • Hermann, T. Aminoglycoside antibiotics: Old drugs and new therapeutic approaches. Cell. Mol. Life Sci. 2007, 64, 1841-52.
    • (2007) Cell. Mol. Life Sci , vol.64 , pp. 1841-1852
    • Hermann, T.1
  • 4
    • 0034699519 scopus 로고    scopus 로고
    • Functional insights from the structure of the 30s ribosomal subunit and its interactions with antibiotics
    • Carter, A. P.; Clemons, W. M.; Brodersen, D. E.; Morgan-Warren, R. J.; Wimberly, B. T.; Ramakrishnan, V. Functional insights from the structure of the 30s ribosomal subunit and its interactions with antibiotics. Nature 2000, 407, 340-8.
    • (2000) Nature , vol.407 , pp. 340-348
    • Carter, A.P.1    Clemons, W.M.2    Brodersen, D.E.3    Morgan-Warren, R.J.4    Wimberly, B.T.5    Ramakrishnan, V.6
  • 5
    • 0036342198 scopus 로고    scopus 로고
    • The structures of four macrolide antibiotics bound to the large ribosomal subunit
    • Hansen, J. L.; Ippolito, J. A.; Ban, N.; Nissen, P.; Moore, P. B.; Steitz, T. A. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 2002, 10, 117-28.
    • (2002) Mol. Cell , vol.10 , pp. 117-128
    • Hansen, J.L.1    Ippolito, J.A.2    Ban, N.3    Nissen, P.4    Moore, P.B.5    Steitz, T.A.6
  • 7
    • 0034696520 scopus 로고    scopus 로고
    • Aminoglycoside-arginine conjugates that bind tar RNA: Synthesis, characterization, and antiviral activity
    • Litovchick, A.; Evdokimov, A. G.; Lapidot, A. Aminoglycoside-arginine conjugates that bind tar RNA: Synthesis, characterization, and antiviral activity. Biochemistry 2000, 39, 2838-52.
    • (2000) Biochemistry , vol.39 , pp. 2838-2852
    • Litovchick, A.1    Evdokimov, A.G.2    Lapidot, A.3
  • 8
    • 0036008846 scopus 로고    scopus 로고
    • Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target tar RNA
    • Lind, K. E.; Du, Z.; Fujinaga, K.; Peterlin, B. M.; James, T. L. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target tar RNA. Chem. Biol. 2002, 9, 185-93.
    • (2002) Chem. Biol , vol.9 , pp. 185-193
    • Lind, K.E.1    Du, Z.2    Fujinaga, K.3    Peterlin, B.M.4    James, T.L.5
  • 9
    • 0141866666 scopus 로고    scopus 로고
    • Discovery of a small molecule tat-transactivation- responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication
    • Hwang, S.; Tamilarasu, N.; Kibler, K.; Cao, H.; Ali, A.; Ping, Y. H.; Jeang, K. T.; Rana, T. M. Discovery of a small molecule tat-transactivation- responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication. J. Biol. Chem. 2003, 278, 39092-103.
    • (2003) J. Biol. Chem , vol.278 , pp. 39092-39103
    • Hwang, S.1    Tamilarasu, N.2    Kibler, K.3    Cao, H.4    Ali, A.5    Ping, Y.H.6    Jeang, K.T.7    Rana, T.M.8
  • 11
    • 0041836262 scopus 로고    scopus 로고
    • Fluorescence-based methods for evaluating the RNA affinity and specificity of hiv-1 rev-rre inhibitors
    • Luedtke, N. W.; Tor, Y. Fluorescence-based methods for evaluating the RNA affinity and specificity of hiv-1 rev-rre inhibitors. Biopolymers 2003, 70, 103-19.
    • (2003) Biopolymers , vol.70 , pp. 103-119
    • Luedtke, N.W.1    Tor, Y.2
  • 13
    • 0032566484 scopus 로고    scopus 로고
    • Antibiotic inhibition of RNA catalysis: Neomycin b binds to the catalytic core of the td group i intron displacing essential metal ions
    • Hoch, I.; Berens, C.; Westhof, E.; Schroeder, R. Antibiotic inhibition of RNA catalysis: Neomycin b binds to the catalytic core of the td group i intron displacing essential metal ions. J. Mol. Biol. 1998, 282, 557-69.
    • (1998) J. Mol. Biol , vol.282 , pp. 557-569
    • Hoch, I.1    Berens, C.2    Westhof, E.3    Schroeder, R.4
  • 14
    • 0034673532 scopus 로고    scopus 로고
    • Spectinomycin inhibits the self-splicing of the group 1 intron RNA
    • Park, I. K.; Kim, J. Y.; Lim, E. H.; Shin, S. Spectinomycin inhibits the self-splicing of the group 1 intron RNA. Biochem. Biophys. Res. Commun. 2000, 269, 574-9.
    • (2000) Biochem. Biophys. Res. Commun , vol.269 , pp. 574-579
    • Park, I.K.1    Kim, J.Y.2    Lim, E.H.3    Shin, S.4
  • 15
    • 84984569930 scopus 로고    scopus 로고
    • Molecular biology of hepatitis d vims: Research and potential for application
    • Chen, P. J.; Wu, H. L.; Wang, C. J.; Chia, J. H.; Chen, D. S. Molecular biology of hepatitis d vims: Research and potential for application. J. Gastroenterol. Hepatol. 1997, 12, S188-92.
    • (1997) J. Gastroenterol. Hepatol , vol.12
    • Chen, P.J.1    Wu, H.L.2    Wang, C.J.3    Chia, J.H.4    Chen, D.S.5
  • 16
    • 84984575713 scopus 로고    scopus 로고
    • Inhibition of hepatitis delta virus genomic ribozyme self-cleavage by aminoglycosides
    • Chia, J. S.; Wu, H. L.; Wang, H. W.; Chen, D. S.; Chen, P. J. Inhibition of hepatitis delta virus genomic ribozyme self-cleavage by aminoglycosides. J. Biomed. Sci. 1997, 4, 208-16.
    • (1997) J. Biomed. Sci , vol.4 , pp. 208-216
    • Chia, J.S.1    Wu, H.L.2    Wang, H.W.3    Chen, D.S.4    Chen, P.J.5
  • 17
    • 1342300729 scopus 로고    scopus 로고
    • Interactions of the antibiotics neomycin b and Chlortetracycline with the hammerhead ribozyme as studied by zn2+-dependent RNA cleavage
    • Borda, E. J.; Sigurdsson, S. T. Interactions of the antibiotics neomycin b and Chlortetracycline with the hammerhead ribozyme as studied by zn2+-dependent RNA cleavage. Bioorg. Med. Chem. 2004, 12, 1023-8.
    • (2004) Bioorg. Med. Chem , vol.12 , pp. 1023-1028
    • Borda, E.J.1    Sigurdsson, S.T.2
  • 18
    • 33947609739 scopus 로고    scopus 로고
    • Design, synthesis, and evaluation of phenanthridine derivatives targeting the telomerase RNA/DNA heteroduplex
    • Rangarajan, S.; Friedman, S. H. Design, synthesis, and evaluation of phenanthridine derivatives targeting the telomerase RNA/DNA heteroduplex. Bioorg. Med. Chem. Lett. 2007, 17, 2267-73.
    • (2007) Bioorg. Med. Chem. Lett , vol.17 , pp. 2267-2273
    • Rangarajan, S.1    Friedman, S.H.2
  • 19
    • 0030954877 scopus 로고    scopus 로고
    • Structure-based discovery of ligands targeted to the RNA double helix
    • Chen, Q.; Shafer, R. H.; Kuntz, I. D. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry 1997, 36, 11402-7.
    • (1997) Biochemistry , vol.36 , pp. 11402-11407
    • Chen, Q.1    Shafer, R.H.2    Kuntz, I.D.3
  • 21
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • Totrov, M.; Abagyan, R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997, 1, 215-20.
    • (1997) Proteins , vol.1 , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 22
    • 0033443536 scopus 로고    scopus 로고
    • MCSS-based predictions of RNA binding sites
    • Leclerc, F.; Karplus, M. MCSS-based predictions of RNA binding sites. J. Biomol. Struct. Dyn. 1999, 101, 131-37.
    • (1999) J. Biomol. Struct. Dyn , vol.101 , pp. 131-137
    • Leclerc, F.1    Karplus, M.2
  • 23
    • 0031894779 scopus 로고    scopus 로고
    • Modeling RNA-ligand interactions: The rev-binding element RNA-aminoglycoside complex
    • Leclerc, F.; Cedergren, R. Modeling RNA-ligand interactions: The rev-binding element RNA-aminoglycoside complex. J. Med. Chem. 1998, 41, 175-82.
    • (1998) J. Med. Chem , vol.41 , pp. 175-182
    • Leclerc, F.1    Cedergren, R.2
  • 24
    • 0033535566 scopus 로고    scopus 로고
    • Docking of cationic antibiotics to negatively charged pockets in RNA folds
    • Hermann, T.; Westhof, E. Docking of cationic antibiotics to negatively charged pockets in RNA folds. J. Med. Chem. 1999, 42, 1250-61.
    • (1999) J. Med. Chem , vol.42 , pp. 1250-1261
    • Hermann, T.1    Westhof, E.2
  • 25
    • 1842450536 scopus 로고    scopus 로고
    • NMR-based characterization of phenothiazines as a RNA binding scaffold
    • Mayer, M.; James, T. L. NMR-based characterization of phenothiazines as a RNA binding scaffold. J. Am. Chem. Soc. 2004, 126, 4453-60.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 4453-4460
    • Mayer, M.1    James, T.L.2
  • 26
    • 4043058000 scopus 로고    scopus 로고
    • Validation of an empirical RNA-ligand scoring function for fast flexible docking using ribodock
    • Morley, S. D.; Afshar, M. Validation of an empirical RNA-ligand scoring function for fast flexible docking using ribodock. J. Comput.-Aided Mol. Des. 2004, 18, 189-208.
    • (2004) J. Comput.-Aided Mol. Des , vol.18 , pp. 189-208
    • Morley, S.D.1    Afshar, M.2
  • 27
    • 20444493219 scopus 로고    scopus 로고
    • New inhibitors of the tat-tar RNA interaction found with a "Fuzzy" Pharmacophore model
    • Renner, S.; Ludwig, V.; Boden, O.; Scheffer, U.; Göbel, M.; Schneider, G. New inhibitors of the tat-tar RNA interaction found with a "Fuzzy" Pharmacophore model. ChemBioChem 2005, 6, 1119-25.
    • (2005) ChemBioChem , vol.6 , pp. 1119-1125
    • Renner, S.1    Ludwig, V.2    Boden, O.3    Scheffer, U.4    Göbel, M.5    Schneider, G.6
  • 28
    • 25444479686 scopus 로고    scopus 로고
    • Design, synthesis and bioactivities of tar RNA targeting beta-carboline derivatives based on tat-tar interaction
    • Yu, X.; Lin, W.; Pang, R.; Yang, M. Design, synthesis and bioactivities of tar RNA targeting beta-carboline derivatives based on tat-tar interaction. Eur. J. Med. Chem. 2005, 40, 831-9.
    • (2005) Eur. J. Med. Chem , vol.40 , pp. 831-839
    • Yu, X.1    Lin, W.2    Pang, R.3    Yang, M.4
  • 29
    • 33748561836 scopus 로고    scopus 로고
    • Synthesis and testing of a focused phenothiazine library for binding to hiv-1 tar RNA
    • Mayer, M.; Lang, P. T.; Gerber, S.; Madrid, P. B.; Gómez Pinto, I.; Guy, R. K.; James, T. L. Synthesis and testing of a focused phenothiazine library for binding to hiv-1 tar RNA. Chem. Biol. 2006, 13, 993-1000.
    • (2006) Chem. Biol , vol.13 , pp. 993-1000
    • Mayer, M.1    Lang, P.T.2    Gerber, S.3    Madrid, P.B.4    Gómez Pinto, I.5    Guy, R.K.6    James, T.L.7
  • 30
    • 3843057001 scopus 로고    scopus 로고
    • Validation of automated docking programs for docking and database screening against RNA drug targets
    • Detering, C.; Varani, G. Validation of automated docking programs for docking and database screening against RNA drug targets. J. Med. Chem. 2004, 47, 4188-201.
    • (2004) J. Med. Chem , vol.47 , pp. 4188-4201
    • Detering, C.1    Varani, G.2
  • 31
    • 32344449937 scopus 로고    scopus 로고
    • Docking of aminoglycosides to hydrated and flexible RNA
    • Moitessier, N.; Westhof, E.; Hanessian, S. Docking of aminoglycosides to hydrated and flexible RNA. J. Med. Chem. 2006, 49, 1023-33.
    • (2006) J. Med. Chem , vol.49 , pp. 1023-1033
    • Moitessier, N.1    Westhof, E.2    Hanessian, S.3
  • 32
    • 35248883964 scopus 로고    scopus 로고
    • rna-knowledge-based scoring function to predict RNA-ligand interactions
    • rna-knowledge-based scoring function to predict RNA-ligand interactions. J. Chem. Inf. Model. 2007, 47, 1868-76.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1868-1876
    • Pfeffer, P.1    Gohlke, H.2
  • 33
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4
    • Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4. J. Comput.-Aided Mol. Des. 1996, 10, 293-304.
    • (1996) J. Comput.-Aided Mol. Des , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 34
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-25.
    • (2004) J. Mol. Biol , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 35
    • 0032189738 scopus 로고    scopus 로고
    • Small structural ensembles for a 17-nucleotide mimic of the tma t psi c-loop via fitting dipolar relaxation rates with the quadratic programming algorithm
    • Schmitz, U.; Donati, A.; James, T. L.; Ulyanov, N. B.; Yao, L. Small structural ensembles for a 17-nucleotide mimic of the tma t psi c-loop via fitting dipolar relaxation rates with the quadratic programming algorithm. Biopolymers 1998, 46, 329-42.
    • (1998) Biopolymers , vol.46 , pp. 329-342
    • Schmitz, U.1    Donati, A.2    James, T.L.3    Ulyanov, N.B.4    Yao, L.5
  • 36
    • 47349125648 scopus 로고    scopus 로고
    • Conformational ensemble calculations: Analysis of protein and nucleic acid NMR data
    • Krishna, N. R, Berliner, L. J, Eds, Kluwer Academic: New York
    • Mujeeb, A.; Ulyanov, N. B.; Billed, T. M.; Farr-Jones, S.; James, T. L. Conformational ensemble calculations: Analysis of protein and nucleic acid NMR data. In Biological magnetic resonance; Krishna, N. R., Berliner, L. J., Eds.; Kluwer Academic: New York, 1999; Vol. 17, pp 201-20.
    • (1999) Biological magnetic resonance , vol.17 , pp. 201-220
    • Mujeeb, A.1    Ulyanov, N.B.2    Billed, T.M.3    Farr-Jones, S.4    James, T.L.5
  • 37
    • 0035432947 scopus 로고    scopus 로고
    • Molecular recognition by induced fit: How fit is the concept
    • Bosshard, H. R. Molecular recognition by induced fit: How fit is the concept. News Physiol. Sci. 2001, 16, 171-3.
    • (2001) News Physiol. Sci , vol.16 , pp. 171-173
    • Bosshard, H.R.1
  • 38
    • 34447271743 scopus 로고    scopus 로고
    • Exploring experimental sources of multiple protein conformations in structure-based drug design
    • Damm, K. L.; Carlson, H. A. Exploring experimental sources of multiple protein conformations in structure-based drug design. J. Am. Chem. Soc. 2007, 729, 8225-35.
    • (2007) J. Am. Chem. Soc , vol.729 , pp. 8225-8235
    • Damm, K.L.1    Carlson, H.A.2
  • 39
    • 34548200847 scopus 로고    scopus 로고
    • Structure-based drug design: Docking and scoring
    • Kroemer, R. T. Structure-based drug design: Docking and scoring. Curr. Protein Pept. Sci. 2007, 8, 312-28.
    • (2007) Curr. Protein Pept. Sci , vol.8 , pp. 312-328
    • Kroemer, R.T.1
  • 41
    • 34547661861 scopus 로고    scopus 로고
    • Comparative performance of several flexible docking programs and scoring functions: Enrichment studies for a diverse set of pharmaceutically relevant targets
    • Zhou, Z.; Felts, A. K.; Friesner, R. A.; Levy, R. M. Comparative performance of several flexible docking programs and scoring functions: Enrichment studies for a diverse set of pharmaceutically relevant targets. J. Chem. Inf. Model. 2007, 47, 1599-608.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1599-1608
    • Zhou, Z.1    Felts, A.K.2    Friesner, R.A.3    Levy, R.M.4
  • 42
    • 14744276066 scopus 로고    scopus 로고
    • Flexible docking in solution using metadynamics
    • Gervasio, F. L.; Laio, A.; Parrinello, M. Flexible docking in solution using metadynamics. J. Am. Chem. Soc. 2005, 127, 2600-7.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 2600-2607
    • Gervasio, F.L.1    Laio, A.2    Parrinello, M.3
  • 43
    • 33745088619 scopus 로고    scopus 로고
    • Use of an induced fit receptor structure in virtual screening
    • Sherman, W.; Beard, H. S.; Farid, R. Use of an induced fit receptor structure in virtual screening. Chem. Biol. Drug Des. 2006, 67, 83-4.
    • (2006) Chem. Biol. Drug Des , vol.67 , pp. 83-84
    • Sherman, W.1    Beard, H.S.2    Farid, R.3
  • 44
    • 34247197110 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 1. Development and validation of fitted 1.0
    • Corbeil, C. R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of fitted 1.0. J. Chem. Inf. Model. 2007, 47, 435-49.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 435-449
    • Corbeil, C.R.1    Englebienne, P.2    Moitessier, N.3
  • 45
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 2004, 47, 5076-84.
    • (2004) J. Med. Chem , vol.47 , pp. 5076-5084
    • Ferrari, A.M.1    Wei, B.Q.2    Costantino, L.3    Shoichet, B.K.4
  • 46
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-40.
    • (1997) J. Mol. Biol , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 47
    • 0035957528 scopus 로고    scopus 로고
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. Flexe: Efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-95.
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. Flexe: Efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-95.
  • 48
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in autodock
    • Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in autodock. Proteins 2002, 46, 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 49
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
    • (2004) J. Med. Chem , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 50
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • Lin, J.-H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J. Am. Chem. Soc. 2002, 124, 5632-3.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 5632-5633
    • Lin, J.-H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 51
    • 0037231646 scopus 로고    scopus 로고
    • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    • Lin, J.-H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003, 68, 47-62.
    • (2003) Biopolymers , vol.68 , pp. 47-62
    • Lin, J.-H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 52
    • 33745880692 scopus 로고    scopus 로고
    • Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 map kinase
    • Frembgen-Kesner, T.; Elcock, A. H. Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 map kinase. J. Mol. Biol. 2006, 359, 202-14.
    • (2006) J. Mol. Biol , vol.359 , pp. 202-214
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 53
    • 0035915338 scopus 로고    scopus 로고
    • Fully flexible low-mode docking: Application to induced fit in hiv integrase
    • Keserû, G. M.; Kolossváry, I. Fully flexible low-mode docking: Application to induced fit in hiv integrase. J. Am. Chem. Soc. 2001, 123, 12708-9.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 12708-12709
    • Keserû, G.M.1    Kolossváry, I.2
  • 54
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 2005, 127, 9632-40.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 55
    • 33748759844 scopus 로고    scopus 로고
    • Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors
    • Floquet, N.; Marechal, J. D.; Badet-Denisot, M. A.; Robert, C. H.; Dauchez, M.; Perahia, D. Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors. FEBS Lett. 2006, 580, 5130-6.
    • (2006) FEBS Lett , vol.580 , pp. 5130-5136
    • Floquet, N.1    Marechal, J.D.2    Badet-Denisot, M.A.3    Robert, C.H.4    Dauchez, M.5    Perahia, D.6
  • 56
    • 0026614434 scopus 로고
    • The t< - >r structural transition of insulin; pathways suggested by targeted energy minimization
    • Engels, M.; Jacoby, E.; Krüger, P.; Schlitter, J.; Wollmer, A. The t< - >r structural transition of insulin; pathways suggested by targeted energy minimization. Protein Eng. 1992, 5, 669-77.
    • (1992) Protein Eng , vol.5 , pp. 669-677
    • Engels, M.1    Jacoby, E.2    Krüger, P.3    Schlitter, J.4    Wollmer, A.5
  • 57
    • 0029633176 scopus 로고
    • A method to explore transition paths in macromolecules. Application to hemoglobin and phosphoglycerate kinase
    • Guilbert, C.; Perahia, D.; Mouawad, L. A method to explore transition paths in macromolecules. Application to hemoglobin and phosphoglycerate kinase. Comp. Phys. Com. 1995, 91, 263-73.
    • (1995) Comp. Phys. Com , vol.91 , pp. 263-273
    • Guilbert, C.1    Perahia, D.2    Mouawad, L.3
  • 58
    • 0242593434 scopus 로고    scopus 로고
    • Development and current status of the charmm force field for nucleic acids
    • MacKerell, A. D.; Banavali, N.; Foloppe, N. Development and current status of the charmm force field for nucleic acids. Biopolymers 2000, 56, 257-65.
    • (2000) Biopolymers , vol.56 , pp. 257-265
    • MacKerell, A.D.1    Banavali, N.2    Foloppe, N.3
  • 61
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 2006, 25, 247-260.
    • (2006) J. Mol. Graphics Modell , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 64
    • 0141956090 scopus 로고    scopus 로고
    • Im, W.; Lee, M. S.; Brooks, C. L. 3rd Generalized bom model with a simple smoothing function. J. Comput. Chem. 2003, 24, 1691-702.
    • Im, W.; Lee, M. S.; Brooks, C. L. 3rd Generalized bom model with a simple smoothing function. J. Comput. Chem. 2003, 24, 1691-702.
  • 65
    • 0343550557 scopus 로고    scopus 로고
    • Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights
    • Görler, A.; Ulyanov, N. B.; James, T. L. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights. /. Biomol. NMR 2000, 16, 147-64.
    • (2000) Biomol. NMR , vol.16 , pp. 147-164
    • Görler, A.1    Ulyanov, N.B.2    James, T.L.3
  • 66
    • 0037330568 scopus 로고    scopus 로고
    • Encapsulating streptomycin within a small 40-mer RNA
    • Tereshko, V.; Skripkin, E.; Patel, D. J. Encapsulating streptomycin within a small 40-mer RNA. Chem. Biol. 2003, 10, 175-87.
    • (2003) Chem. Biol , vol.10 , pp. 175-187
    • Tereshko, V.1    Skripkin, E.2    Patel, D.J.3
  • 68
    • 34248358986 scopus 로고    scopus 로고
    • Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions
    • Ruvinsky, A.M. Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions. J. Comput. Chem. 2007, 28, 1364-72.
    • (2007) J. Comput. Chem , vol.28 , pp. 1364-1372
    • Ruvinsky, A.M.1


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