메뉴 건너뛰기




Volumn 254, Issue 2, 2008, Pages 294-300

Analysis of ligand binding to proteins using molecular dynamics simulations

Author keywords

Bovine carbonic anhydrase; Cobra cardiotoxin; Lysozyme; Sodium dodecyl sulfate; Thiourea

Indexed keywords

CARBONATE DEHYDRATASE; COBROTOXIN; DODECYL SULFATE SODIUM; LYSOZYME; THIOUREA;

EID: 50149091918     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.04.036     Document Type: Article
Times cited : (44)

References (73)
  • 1
    • 3042549928 scopus 로고
    • Binding affinity prediction with different force fields: examination of the linear interaction energy method
    • Almlöf M., Brandsdal B.O., and Åqvist J. Binding affinity prediction with different force fields: examination of the linear interaction energy method. J. Comput. Chem. 25 (1994) 1242-1254
    • (1994) J. Comput. Chem. , vol.25 , pp. 1242-1254
    • Almlöf, M.1    Brandsdal, B.O.2    Åqvist, J.3
  • 4
    • 36449003225 scopus 로고
    • Molecular dynamics free energy calculation in four dimensions
    • Beutler T.C., and van Gunsteren W.F. Molecular dynamics free energy calculation in four dimensions. J. Chem. Phys. 101 (1994) 1417-1422
    • (1994) J. Chem. Phys. , vol.101 , pp. 1417-1422
    • Beutler, T.C.1    van Gunsteren, W.F.2
  • 5
    • 10344247720 scopus 로고    scopus 로고
    • MD simulations of spontaneous membrane protein/detergent micelle formation
    • Bond P.J., Cuthbertson J.M., Deol S.S., and Sanson M.S.P. MD simulations of spontaneous membrane protein/detergent micelle formation. J. Am. Chem. Soc. 126 (2004) 15948-15949
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 15948-15949
    • Bond, P.J.1    Cuthbertson, J.M.2    Deol, S.S.3    Sanson, M.S.P.4
  • 6
    • 3242792729 scopus 로고    scopus 로고
    • Review: structural bioinformatics and its impact to biomedical science
    • Chou K.C. Review: structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11 (2004) 2105-2134
    • (2004) Curr. Med. Chem. , vol.11 , pp. 2105-2134
    • Chou, K.C.1
  • 7
    • 0041848237 scopus 로고    scopus 로고
    • Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS
    • (Erratum: ibid, 2003, vol. 310, p. 675)
    • Chou K.C., Wei D.Q., and Zhong W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun. 308 (2003) 148-151 (Erratum: ibid, 2003, vol. 310, p. 675)
    • (2003) Biochem. Biophys. Res. Commun. , vol.308 , pp. 148-151
    • Chou, K.C.1    Wei, D.Q.2    Zhong, W.Z.3
  • 8
    • 33750554701 scopus 로고    scopus 로고
    • Review: progress in computational approach to drug development against SARS
    • Chou K.C., Wei D.Q., Du Q.S., Sirois S., and Zhong W.Z. Review: progress in computational approach to drug development against SARS. Curr. Med. Chem. 13 (2006) 3263-3270
    • (2006) Curr. Med. Chem. , vol.13 , pp. 3263-3270
    • Chou, K.C.1    Wei, D.Q.2    Du, Q.S.3    Sirois, S.4    Zhong, W.Z.5
  • 9
    • 33644884977 scopus 로고    scopus 로고
    • Insight into the structure of Mesorhizobium lotiarylamine N-acetyltransferase 2 (MLNAT2): a biological and computational study
    • Dairou J., Flatters D., Chaffotte A.F., Pluvinage B., Sim E., Dupert J.M., and Lima F.R. Insight into the structure of Mesorhizobium lotiarylamine N-acetyltransferase 2 (MLNAT2): a biological and computational study. FEBS Lett. 580 (2006) 1780-1788
    • (2006) FEBS Lett. , vol.580 , pp. 1780-1788
    • Dairou, J.1    Flatters, D.2    Chaffotte, A.F.3    Pluvinage, B.4    Sim, E.5    Dupert, J.M.6    Lima, F.R.7
  • 10
    • 9744256949 scopus 로고    scopus 로고
    • Structural stability of wide type and mutated α-Keratin fragments: molecular dynamics and free energy calculations
    • Danciulescu C., Nike B., and Wortmann F.J. Structural stability of wide type and mutated α-Keratin fragments: molecular dynamics and free energy calculations. Biomacromolecules 5 (2004) 2165-2175
    • (2004) Biomacromolecules , vol.5 , pp. 2165-2175
    • Danciulescu, C.1    Nike, B.2    Wortmann, F.J.3
  • 11
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an N log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 12
    • 33947316105 scopus 로고    scopus 로고
    • The effect of sodium dodecyl sulfate on the conformation of bovine serum albumin
    • Ding Y., Shu Y., Ge L., and Guo R. The effect of sodium dodecyl sulfate on the conformation of bovine serum albumin. Colloids Surf. A: Physicochem. Eng. Aspects 298 (2007) 163-169
    • (2007) Colloids Surf. A: Physicochem. Eng. Aspects , vol.298 , pp. 163-169
    • Ding, Y.1    Shu, Y.2    Ge, L.3    Guo, R.4
  • 13
    • 11844253806 scopus 로고    scopus 로고
    • Flavonoid-serum albumin complexation: determination of binding constants and binding sites by fluorescence spectroscopy
    • Dufour C., and Dangles O. Flavonoid-serum albumin complexation: determination of binding constants and binding sites by fluorescence spectroscopy. Biochim. Biophys. Acta 1721 (2005) 164-173
    • (2005) Biochim. Biophys. Acta , vol.1721 , pp. 164-173
    • Dufour, C.1    Dangles, O.2
  • 14
    • 6344236941 scopus 로고    scopus 로고
    • Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of octapeptide
    • Du Q.S., Wang S.Q., Wei D.Q., Zhu Y., Guo H., Sirois S., and Chou K.C. Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of octapeptide. Peptides 25 (2004) 1857-1864
    • (2004) Peptides , vol.25 , pp. 1857-1864
    • Du, Q.S.1    Wang, S.Q.2    Wei, D.Q.3    Zhu, Y.4    Guo, H.5    Sirois, S.6    Chou, K.C.7
  • 15
    • 13244290092 scopus 로고    scopus 로고
    • Molecular modelling and chemical modification for finding peptide inhibitor against SARS CoV Mpro
    • Du Q.S., Wang S., Wei D.Q., Sirois S., and Chou K.C. Molecular modelling and chemical modification for finding peptide inhibitor against SARS CoV Mpro. Anal. Biochem. 337 (2005) 262-270
    • (2005) Anal. Biochem. , vol.337 , pp. 262-270
    • Du, Q.S.1    Wang, S.2    Wei, D.Q.3    Sirois, S.4    Chou, K.C.5
  • 16
    • 26844549522 scopus 로고    scopus 로고
    • Application of bioinformatics in search for cleavable peptides of SARS-CoV Mpro and chemical modification of octapeptides
    • Du Q.S., Wang S.Q., Jiang Z.Q., Gao W.N., Li Y.D., Wei D.Q., and Chou K.C. Application of bioinformatics in search for cleavable peptides of SARS-CoV Mpro and chemical modification of octapeptides. Med. Chem. 1 (2005) 209-213
    • (2005) Med. Chem. , vol.1 , pp. 209-213
    • Du, Q.S.1    Wang, S.Q.2    Jiang, Z.Q.3    Gao, W.N.4    Li, Y.D.5    Wei, D.Q.6    Chou, K.C.7
  • 17
    • 34548261773 scopus 로고    scopus 로고
    • Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus
    • Du Q.S., Wang S.Q., and Chou K.C. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem. Biophys. Res. Commun. 362 (2007) 525-531
    • (2007) Biochem. Biophys. Res. Commun. , vol.362 , pp. 525-531
    • Du, Q.S.1    Wang, S.Q.2    Chou, K.C.3
  • 18
    • 0033545623 scopus 로고    scopus 로고
    • Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations
    • Eriksson M.A., Pitera J., and Kollman P.A. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. J. Med. Chem. 42 (1999) 868-881
    • (1999) J. Med. Chem. , vol.42 , pp. 868-881
    • Eriksson, M.A.1    Pitera, J.2    Kollman, P.A.3
  • 20
    • 0038695001 scopus 로고    scopus 로고
    • Effects of pathological mutations on the stability of a conserved amino acid triad in ritinoschisin
    • Fraternali F., Cavallo L., and Giovanna M. Effects of pathological mutations on the stability of a conserved amino acid triad in ritinoschisin. FEBS Lett. 544 (2003) 21-26
    • (2003) FEBS Lett. , vol.544 , pp. 21-26
    • Fraternali, F.1    Cavallo, L.2    Giovanna, M.3
  • 21
    • 34248679618 scopus 로고    scopus 로고
    • Agaritine and its derivatives are potential inhibitors against HIV proteases
    • Gao W.N., Wei D.Q., Li Y., Gao H., Xu W.R., Li A.X., and Chou K.C. Agaritine and its derivatives are potential inhibitors against HIV proteases. Med. Chem. 3 (2007) 221-226
    • (2007) Med. Chem. , vol.3 , pp. 221-226
    • Gao, W.N.1    Wei, D.Q.2    Li, Y.3    Gao, H.4    Xu, W.R.5    Li, A.X.6    Chou, K.C.7
  • 22
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: a critical review
    • Gilson M.K., Given J.A., Bush B.L., and McCammon J.A. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72 (1997) 1047-1069
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 23
    • 10644231153 scopus 로고    scopus 로고
    • Influence of the Zn (II) cofactor on the refolding of bovine carbonic anhydrase after denaturation with sodium dodecyl sulfate
    • Gudiksen K.L., Gitlin I., Yang J., Urbach A.R., Vazquez J.A., Costello C.E., and Whitesides G.M. Influence of the Zn (II) cofactor on the refolding of bovine carbonic anhydrase after denaturation with sodium dodecyl sulfate. Anal. Chem. 76 (2004) 7151-7161
    • (2004) Anal. Chem. , vol.76 , pp. 7151-7161
    • Gudiksen, K.L.1    Gitlin, I.2    Yang, J.3    Urbach, A.R.4    Vazquez, J.A.5    Costello, C.E.6    Whitesides, G.M.7
  • 24
    • 33745752989 scopus 로고    scopus 로고
    • Increasing the net charge and decreasing the hydrophobicity of bovine carbonic anhydrase decreases the rate of denaturation with sodium dodecyl sulfate
    • Gudiksen K.L., Gitlin I., Moustakas D.T., and Whitesides G.M. Increasing the net charge and decreasing the hydrophobicity of bovine carbonic anhydrase decreases the rate of denaturation with sodium dodecyl sulfate. Biophys. J. 91 (2006) 298-310
    • (2006) Biophys. J. , vol.91 , pp. 298-310
    • Gudiksen, K.L.1    Gitlin, I.2    Moustakas, D.T.3    Whitesides, G.M.4
  • 25
    • 49749097226 scopus 로고    scopus 로고
    • Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin
    • 10.1007/s00726-007-0611-3
    • Guo X.L., Li L., Wei D.Q., Zhu Y.S., and Chou K.C. Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids (2007) 10.1007/s00726-007-0611-3
    • (2007) Amino Acids
    • Guo, X.L.1    Li, L.2    Wei, D.Q.3    Zhu, Y.S.4    Chou, K.C.5
  • 26
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M., Rippmann F., and Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 15 (1997) 359-363
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 28
    • 84944486386 scopus 로고
    • A new mathematical treatment of changes of ionic concentration in muscle and nerve under the action of electric currents, with a theory as to their mode of excitation
    • Hill A.V. A new mathematical treatment of changes of ionic concentration in muscle and nerve under the action of electric currents, with a theory as to their mode of excitation. J. Physiol. 40 (1910) 190-224
    • (1910) J. Physiol. , vol.40 , pp. 190-224
    • Hill, A.V.1
  • 29
    • 0028273592 scopus 로고
    • Determination of binding affinities of glucose oxidase for sodium n-dodecyl sulfate
    • Housaindokht M.R., and Moosavi-Movahedi A.A. Determination of binding affinities of glucose oxidase for sodium n-dodecyl sulfate. Int. J. Biol. Macromol. 16 2 (1994) 77-80
    • (1994) Int. J. Biol. Macromol. , vol.16 , Issue.2 , pp. 77-80
    • Housaindokht, M.R.1    Moosavi-Movahedi, A.A.2
  • 32
    • 23044497761 scopus 로고    scopus 로고
    • A differential scanning calorimetric study of the influence of copper and dodecyl trimethyl ammonium bromide on the stability of bovine α-lactalbumin
    • Housaindokht M.R., Chamani J., and Moosavi-Movahedi A.A. A differential scanning calorimetric study of the influence of copper and dodecyl trimethyl ammonium bromide on the stability of bovine α-lactalbumin. Int. J. Biol. Macromol. 36 3 (2005) 169-175
    • (2005) Int. J. Biol. Macromol. , vol.36 , Issue.3 , pp. 169-175
    • Housaindokht, M.R.1    Chamani, J.2    Moosavi-Movahedi, A.A.3
  • 34
    • 33750029942 scopus 로고    scopus 로고
    • csc: predicting ligand binding sites using the Connolly surface and degree of conservation
    • csc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 6 (2006) 19-30
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19-30
    • Huang, B.1    Schroeder, M.2
  • 35
    • 0001684352 scopus 로고
    • Surfactants interactions with biomembranes and proteins
    • Jones M.N. Surfactants interactions with biomembranes and proteins. Chem. Soc. Rev. 21 (1992) 127-136
    • (1992) Chem. Soc. Rev. , vol.21 , pp. 127-136
    • Jones, M.N.1
  • 36
    • 0003956181 scopus 로고
    • Food polymers, gels, and colloids
    • Dickinson E. (Ed), The Royal Society of Chemistry, Cambridge
    • Jones M.N., and Brass A. Food polymers, gels, and colloids. In: Dickinson E. (Ed). Special Publication No. 82 (1991), The Royal Society of Chemistry, Cambridge 65
    • (1991) Special Publication No. 82 , pp. 65
    • Jones, M.N.1    Brass, A.2
  • 38
    • 7044239742 scopus 로고
    • Free energy calculations: applications to chemical and biochemical phenomena
    • Kollman P. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93 (1993) 2395-2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 39
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions
    • Laskowski R. SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. 13 (1995) 323-330
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-330
    • Laskowski, R.1
  • 40
    • 1842788183 scopus 로고    scopus 로고
    • Interaction of amiloride and one of its derivatives with Vpu from HIV-1: a molecular dynamics simulation
    • Lemaitre V., Ali R., Kim C.G., Watts A., and Fischer W.B. Interaction of amiloride and one of its derivatives with Vpu from HIV-1: a molecular dynamics simulation. FEBS Lett. 563 (2004) 75-81
    • (2004) FEBS Lett. , vol.563 , pp. 75-81
    • Lemaitre, V.1    Ali, R.2    Kim, C.G.3    Watts, A.4    Fischer, W.B.5
  • 41
    • 0027053611 scopus 로고
    • POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • Levitt D., and Banaszak L. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph. 10 (1992) 229-234
    • (1992) J. Mol. Graph. , vol.10 , pp. 229-234
    • Levitt, D.1    Banaszak, L.2
  • 42
    • 34249743013 scopus 로고    scopus 로고
    • Computational studies of the binding mechanism of calmodulin with chrysin
    • Li L., Wei D.Q., Wang J.F., and Chou K.C. Computational studies of the binding mechanism of calmodulin with chrysin. Biochem. Biophys. Res. Commun. 358 (2007) 1102-1107
    • (2007) Biochem. Biophys. Res. Commun. , vol.358 , pp. 1102-1107
    • Li, L.1    Wei, D.Q.2    Wang, J.F.3    Chou, K.C.4
  • 44
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design
    • Liang J., Edelsbrunner H., and Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7 (1998) 1884-1897
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 45
    • 0029633168 scopus 로고
    • A message-passing parallel molecular dynamics implementation
    • Lindahl E., Hess B., and van der Spoel D. A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91 (1995) 43-56
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 43-56
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 46
    • 27844598851 scopus 로고    scopus 로고
    • Searching for hypothetical proteins: theory and practice based upon original data and literature
    • Lubec G., Afjehi-Sadat L., Yang J.W., and John J.P. Searching for hypothetical proteins: theory and practice based upon original data and literature. Prog. Neurobiol. 77 (2005) 90-127
    • (2005) Prog. Neurobiol. , vol.77 , pp. 90-127
    • Lubec, G.1    Afjehi-Sadat, L.2    Yang, J.W.3    John, J.P.4
  • 47
    • 84986440341 scopus 로고
    • Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miamoto S., and Kollman P.A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13 (1992) 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miamoto, S.1    Kollman, P.A.2
  • 48
    • 1942532321 scopus 로고    scopus 로고
    • Comuter simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor
    • Monticelli L., Robertson K.M., MacCallum J.L., and Tieleman D.P. Comuter simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor. FEBS Lett. 564 (2004) 325-332
    • (2004) FEBS Lett. , vol.564 , pp. 325-332
    • Monticelli, L.1    Robertson, K.M.2    MacCallum, J.L.3    Tieleman, D.P.4
  • 49
    • 0025620348 scopus 로고
    • Thermodynamics studies on the interaction between sodium n-dodecyl sulphate and histone H2B
    • Moosavi-Movahedi A.A., and Housaindokht M.R. Thermodynamics studies on the interaction between sodium n-dodecyl sulphate and histone H2B. Physiol. Chem. Phys. Med. NMR 22 1 (1990) 19-26
    • (1990) Physiol. Chem. Phys. Med. NMR , vol.22 , Issue.1 , pp. 19-26
    • Moosavi-Movahedi, A.A.1    Housaindokht, M.R.2
  • 50
    • 0032698313 scopus 로고    scopus 로고
    • Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method
    • Pearlman D.A. Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method. J. Med. Chem. 42 (1999) 4313-4324
    • (1999) J. Med. Chem. , vol.42 , pp. 4313-4324
    • Pearlman, D.A.1
  • 51
    • 33746657174 scopus 로고    scopus 로고
    • MD simulations of mistic: conformational stability in detergent micelles and water
    • Psachoulia E., Bond P.J., and Sanson M.S.P. MD simulations of mistic: conformational stability in detergent micelles and water. Biochemistry 45 (2006) 9053-9058
    • (2006) Biochemistry , vol.45 , pp. 9053-9058
    • Psachoulia, E.1    Bond, P.J.2    Sanson, M.S.P.3
  • 52
    • 0032058875 scopus 로고    scopus 로고
    • The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors
    • Randmer R.J., and Kollman P.A. The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. J. Comput.-Aided Mol. Des. 12 (1998) 215-227
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 215-227
    • Randmer, R.J.1    Kollman, P.A.2
  • 54
    • 33646512405 scopus 로고    scopus 로고
    • On the edge of the denaturation process: application of X-ray differaction to barnase and lysozyme cross-linked crystals with denaturants in molar concentration
    • Salem M., Mauguen Y., and Prange T. On the edge of the denaturation process: application of X-ray differaction to barnase and lysozyme cross-linked crystals with denaturants in molar concentration. Biochim. Biophys. Acta 1746 (2006) 903-912
    • (2006) Biochim. Biophys. Acta , vol.1746 , pp. 903-912
    • Salem, M.1    Mauguen, Y.2    Prange, T.3
  • 55
    • 84969001783 scopus 로고
    • The attractions of proteins for small molecules and ions
    • Scatchard G. The attractions of proteins for small molecules and ions. Ann. N Y Acad. Sci. 51 (1949) 660-672
    • (1949) Ann. N Y Acad. Sci. , vol.51 , pp. 660-672
    • Scatchard, G.1
  • 56
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins
    • Shirts M.R., Pitera J.W., Swope W.C., and Pande V.S. Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins. J. Chem. Phys. 119 (2003) 5740-5761
    • (2003) J. Chem. Phys. , vol.119 , pp. 5740-5761
    • Shirts, M.R.1    Pitera, J.W.2    Swope, W.C.3    Pande, V.S.4
  • 57
    • 2942750460 scopus 로고    scopus 로고
    • Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points
    • Sirois S., Wei D.Q., Du Q.S., and Chou K.C. Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points. J. Chem. Inf. Comput. Sci. 44 (2004) 1111-1122
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 1111-1122
    • Sirois, S.1    Wei, D.Q.2    Du, Q.S.3    Chou, K.C.4
  • 58
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: survey for simulating the activity of proteins
    • Stewart A.A., and McCammon J.A. Molecular dynamics: survey for simulating the activity of proteins. Chem. Rev. 106 (2006) 1589-1615
    • (2006) Chem. Rev. , vol.106 , pp. 1589-1615
    • Stewart, A.A.1    McCammon, J.A.2
  • 60
    • 50149085765 scopus 로고    scopus 로고
    • van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., Kruger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G., 1996. Biomolecular Simulation: The Gromos96 Manual and User Guide. Hochschulverlag AG an der ETH, Zurich.
    • van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., Kruger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G., 1996. Biomolecular Simulation: The Gromos96 Manual and User Guide. Hochschulverlag AG an der ETH, Zurich.
  • 61
    • 33847129220 scopus 로고    scopus 로고
    • 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design
    • (Corrigendum: ibid, 2007, Vol. 357, p. 330)
    • Wang J.F., Wei D.Q., Li L., Zheng S.Y., Li Y.X., and Chou K.C. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem. Biophys. Res. Commun. 355 (2007) 513-519 (Corrigendum: ibid, 2007, Vol. 357, p. 330)
    • (2007) Biochem. Biophys. Res. Commun. , vol.355 , pp. 513-519
    • Wang, J.F.1    Wei, D.Q.2    Li, L.3    Zheng, S.Y.4    Li, Y.X.5    Chou, K.C.6
  • 62
    • 34249993539 scopus 로고    scopus 로고
    • Insights from modeling the 3D structure of NAD(P)H-dependent d-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP
    • Wang J.F., Wei D.Q., Lin Y., Wang Y.H., Du H.L., Li Y.X., and Chou K.C. Insights from modeling the 3D structure of NAD(P)H-dependent d-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun. 359 (2007) 323-329
    • (2007) Biochem. Biophys. Res. Commun. , vol.359 , pp. 323-329
    • Wang, J.F.1    Wei, D.Q.2    Lin, Y.3    Wang, Y.H.4    Du, H.L.5    Li, Y.X.6    Chou, K.C.7
  • 63
    • 33846617350 scopus 로고    scopus 로고
    • Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases
    • Wang S.Q., Du Q.S., and Chou K.C. Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem. Biophys. Res. Commun. 354 (2007) 634-640
    • (2007) Biochem. Biophys. Res. Commun. , vol.354 , pp. 634-640
    • Wang, S.Q.1    Du, Q.S.2    Chou, K.C.3
  • 64
    • 34547107293 scopus 로고    scopus 로고
    • Virtual screening for finding natural inhibitor against cathepsin-l for SARS therapy
    • Wang S.Q., Du Q.S., Zhao K., Li A.X., Wei D.Q., and Chou K.C. Virtual screening for finding natural inhibitor against cathepsin-l for SARS therapy. Amino Acids 33 (2007) 129-135
    • (2007) Amino Acids , vol.33 , pp. 129-135
    • Wang, S.Q.1    Du, Q.S.2    Zhao, K.3    Li, A.X.4    Wei, D.Q.5    Chou, K.C.6
  • 65
    • 38849107581 scopus 로고    scopus 로고
    • Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design
    • Wang J.F., Wei D.Q., Chen C., Li Y., and Chou K.C. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Protein Pept. Lett. 15 (2008) 27-32
    • (2008) Protein Pept. Lett. , vol.15 , pp. 27-32
    • Wang, J.F.1    Wei, D.Q.2    Chen, C.3    Li, Y.4    Chou, K.C.5
  • 66
    • 27744476837 scopus 로고    scopus 로고
    • Theoretical studies of Alzheimer's disease drug candidate [(2,4-dimethoxy) benzylidene]-anabaseine dihydrochloride (GTS-21) and its derivatives
    • Wei D.Q., Sirois S., Du Q.S., Arias H.R., and Chou K.C. Theoretical studies of Alzheimer's disease drug candidate [(2,4-dimethoxy) benzylidene]-anabaseine dihydrochloride (GTS-21) and its derivatives. Biochem. Biophys. Res. Commun. 338 (2005) 1059-1064
    • (2005) Biochem. Biophys. Res. Commun. , vol.338 , pp. 1059-1064
    • Wei, D.Q.1    Sirois, S.2    Du, Q.S.3    Arias, H.R.4    Chou, K.C.5
  • 67
    • 33646160618 scopus 로고    scopus 로고
    • Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands
    • Wei D.Q., Du Q.S., Sun H., and Chou K.C. Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Biochem. Biophys. Res. Commun. 344 (2006) 1048-1055
    • (2006) Biochem. Biophys. Res. Commun. , vol.344 , pp. 1048-1055
    • Wei, D.Q.1    Du, Q.S.2    Sun, H.3    Chou, K.C.4
  • 69
    • 33846449105 scopus 로고    scopus 로고
    • Molecular insights of SAH enzyme catalysis and their implication for inhibitor design
    • Wei H., Zhang R., Wang C., Zheng H., Chou K.C., and Wei D.Q. Molecular insights of SAH enzyme catalysis and their implication for inhibitor design. J. Theor. Biol. 244 (2007) 692-702
    • (2007) J. Theor. Biol. , vol.244 , pp. 692-702
    • Wei, H.1    Zhang, R.2    Wang, C.3    Zheng, H.4    Chou, K.C.5    Wei, D.Q.6
  • 70
    • 0000364298 scopus 로고
    • The binding potential, a neglected linkage concept
    • Wyman J. The binding potential, a neglected linkage concept. J. Mol. Biol. 11 (1965) 631-644
    • (1965) J. Mol. Biol. , vol.11 , pp. 631-644
    • Wyman, J.1
  • 71
    • 47349097287 scopus 로고    scopus 로고
    • Computational studies of the binding modes of A2A adenosine receptor antagonists
    • 10.1007/s00726-007-0604-2
    • Ye Y., Wei J., Dai X., and Gao Q. Computational studies of the binding modes of A2A adenosine receptor antagonists. Amino Acids (2007) 10.1007/s00726-007-0604-2
    • (2007) Amino Acids
    • Ye, Y.1    Wei, J.2    Dai, X.3    Gao, Q.4
  • 72
    • 33746172585 scopus 로고    scopus 로고
    • Molecular modeling studies of peptide drug candidates against SARS
    • Zhang R., Wei D.Q., Du Q.S., and Chou K.C. Molecular modeling studies of peptide drug candidates against SARS. Med. Chem. 2 (2006) 309-314
    • (2006) Med. Chem. , vol.2 , pp. 309-314
    • Zhang, R.1    Wei, D.Q.2    Du, Q.S.3    Chou, K.C.4
  • 73


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.