메뉴 건너뛰기




Volumn 75, Issue 1, 2009, Pages 168-186

Evaluation of an inverse molecular design algorithm in a model binding site

Author keywords

Cytochrome c peroxidase; Dead end elimination; Drug design; Inverse design; Protein ligand interaction; Scoring function

Indexed keywords

AMINE; ANILINIUM DERIVATIVE; CYTOCHROME C PEROXIDASE; MUTANT PROTEIN; PHENOL DERIVATIVE; PROTEIN W191G; UNCLASSIFIED DRUG; WATER;

EID: 65249084628     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22226     Document Type: Article
Times cited : (7)

References (53)
  • 2
    • 3543002852 scopus 로고    scopus 로고
    • Ligand selectivity and competition between enzymes in silico
    • Macchiarulo A, Nobeli I, Thornton JM. Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 2004;22:1039-1045.
    • (2004) Nat Biotechnol , vol.22 , pp. 1039-1045
    • Macchiarulo, A.1    Nobeli, I.2    Thornton, J.M.3
  • 6
    • 0019774747 scopus 로고
    • Molecular engineering: An approach to the development of general capabilities for molecular manipulation
    • Drexler KE. Molecular engineering: an approach to the development of general capabilities for molecular manipulation. Proc Natl Acad Sci USA 1981;78:5275-5278.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 5275-5278
    • Drexler, K.E.1
  • 7
    • 0021108287 scopus 로고
    • Molecular technology. Designing proteins and peptides
    • Pabo C. Molecular technology. Designing proteins and peptides. Nature 1983;301:200.
    • (1983) Nature , vol.301 , pp. 200
    • Pabo, C.1
  • 8
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet J, Demaeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    Demaeyer, M.2    Hazes, B.3    Lasters, I.4
  • 9
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 10
    • 0030886443 scopus 로고    scopus 로고
    • Rational protein design: Combining theory and experiment
    • Hellinga HW. Rational protein design: combining theory and experiment. Proc Natl Acad Sci USA 1997;94:10015-10017.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 10015-10017
    • Hellinga, H.W.1
  • 11
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science 1997;278:82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 13
    • 0031717560 scopus 로고    scopus 로고
    • Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
    • Leach AR, Lemon AP. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Proteins Struct Function Genet 1998;33:227-239.
    • (1998) Proteins Struct Function Genet , vol.33 , pp. 227-239
    • Leach, A.R.1    Lemon, A.P.2
  • 14
    • 34548528158 scopus 로고    scopus 로고
    • Progress in computational protein design
    • Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotechnol 2007;18:305-311.
    • (2007) Curr Opin Biotechnol , vol.18 , pp. 305-311
    • Lippow, S.M.1    Tidor, B.2
  • 15
    • 35148855712 scopus 로고    scopus 로고
    • Computational design of antibody-affinity improvement beyond in vivo maturation
    • Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Bio-technol 2007;25:1171-1176.
    • (2007) Nat Bio-technol , vol.25 , pp. 1171-1176
    • Lippow, S.M.1    Wittrup, K.D.2    Tidor, B.3
  • 16
    • 0001114311 scopus 로고    scopus 로고
    • Conformational splitting: A more powerful criterion for dead-end elimination
    • Pierce NA, Spriet JA, Desmet J, Mayo SL. Conformational splitting: a more powerful criterion for dead-end elimination. J Comput Chem 2000;21:999-1009.
    • (2000) J Comput Chem , vol.21 , pp. 999-1009
    • Pierce, N.A.1    Spriet, J.A.2    Desmet, J.3    Mayo, S.L.4
  • 17
  • 18
    • 0029016268 scopus 로고
    • Energetic origins of specificity of ligand-binding in an interior nonpolar cavity of T4 lysozyme
    • Morton A, Baase WA, Matthews BW. Energetic origins of specificity of ligand-binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 1995;34:8564-8575.
    • (1995) Biochemistry , vol.34 , pp. 8564-8575
    • Morton, A.1    Baase, W.A.2    Matthews, B.W.3
  • 19
    • 0035254959 scopus 로고    scopus 로고
    • Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
    • Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins Struct Function Genet 2001;42:279-293.
    • (2001) Proteins Struct Function Genet , vol.42 , pp. 279-293
    • Su, A.I.1    Lorber, D.M.2    Weston, G.S.3    Baase, W.A.4    Matthews, B.W.5    Shoichet, B.K.6
  • 21
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
    • Deng YQ, Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theory Comput 2006;2:1255-1273.
    • (2006) J Chem Theory Comput , vol.2 , pp. 1255-1273
    • Deng, Y.Q.1    Roux, B.2
  • 23
    • 0028209418 scopus 로고
    • Small-molecule binding to an artificially created cavity at the active-site of cytochrome-c peroxidase
    • Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB. Small-molecule binding to an artificially created cavity at the active-site of cytochrome-c peroxidase. Biochemistry 1994;33:3807-3818.
    • (1994) Biochemistry , vol.33 , pp. 3807-3818
    • Fitzgerald, M.M.1    Churchill, M.J.2    McRee, D.E.3    Goodin, D.B.4
  • 24
    • 0036305832 scopus 로고    scopus 로고
    • Artificial protein cavities as specific ligand-binding templates: Characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein
    • Musah RA, Jensen GM, Bunte SW, Rosenfeld RJ, Goodin DB. Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. J Mol Biol 2002;315:845-857.
    • (2002) J Mol Biol , vol.315 , pp. 845-857
    • Musah, R.A.1    Jensen, G.M.2    Bunte, S.W.3    Rosenfeld, R.J.4    Goodin, D.B.5
  • 25
    • 0346264740 scopus 로고    scopus 로고
    • Automated docking of ligands to an artificial active site: Augmenting crystallographic analysis with computer modeling
    • Rosenfeld RJ, Goodsell DS, Musah RA, Morris GM, Goodin DB, Olson AJ. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J Comput-Aided Mol Des 2003;17:525-536.
    • (2003) J Comput-Aided Mol Des , vol.17 , pp. 525-536
    • Rosenfeld, R.J.1    Goodsell, D.S.2    Musah, R.A.3    Morris, G.M.4    Goodin, D.B.5    Olson, A.J.6
  • 27
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
  • 28
    • 33745599120 scopus 로고    scopus 로고
    • NQ-Flipper: Validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
    • Weichenberger CX, Sippl MJ. NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. Bioinformatics 2006;22:1397-1398.
    • (2006) Bioinformatics , vol.22 , pp. 1397-1398
    • Weichenberger, C.X.1    Sippl, M.J.2
  • 29
    • 84888560529 scopus 로고    scopus 로고
    • Frisch AE, Dennington RD, Keith TA, Nielsen AB, Holder AJ. GaussView, Rev. 3.9. Pittsburg Gaussian Inc.; 2003.
    • Frisch AE, Dennington RD, Keith TA, Nielsen AB, Holder AJ. GaussView, Rev. 3.9. Pittsburg Gaussian Inc.; 2003.
  • 30
    • 0000216860 scopus 로고
    • Solution of the Hartree-Fock equations for polyatomic-molecules by a pseudospectral method
    • Friesner RA. Solution of the Hartree-Fock equations for polyatomic-molecules by a pseudospectral method. J Chem Phys 1987; 86:3522-3531.
    • (1987) J Chem Phys , vol.86 , pp. 3522-3531
    • Friesner, R.A.1
  • 31
    • 84888485233 scopus 로고    scopus 로고
    • Schrödinger Inc. Jaguar 4.1. Portland, OR; 1991-2000.
    • Schrödinger Inc. Jaguar 4.1. Portland, OR; 1991-2000.
  • 32
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 1993;97:10269-10280.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 33
    • 0000667030 scopus 로고
    • Application of RESP charges to calculate conformational energies, hydrogen-bond energies, and free-energies of solvation
    • Cornell WD, Cieplak P, Bayly CI, Kollman PA. Application of RESP charges to calculate conformational energies, hydrogen-bond energies, and free-energies of solvation. J Am Chem Soc 1993;115:9620-9631.
    • (1993) J Am Chem Soc , vol.115 , pp. 9620-9631
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Kollman, P.A.4
  • 34
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free-energies using macroscopic solvent models
    • Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J Phys Chem 1994; 98:1978-1988.
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 35
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct Function Genet 1988;4:7-18.
    • (1988) Proteins Struct Function Genet , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 36
    • 84888542707 scopus 로고    scopus 로고
    • Frisch MJT, GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scal-mani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C. 02. 2004
    • Frisch MJT, GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scal-mani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C. 02. 2004.
  • 37
    • 0141570842 scopus 로고    scopus 로고
    • Evaluation of ab initio charge determination methods for use in continuum solvation calculations
    • Green DF, Tidor B. Evaluation of ab initio charge determination methods for use in continuum solvation calculations. J Phys Chem B 2003;107:10261-10273.
    • (2003) J Phys Chem B , vol.107 , pp. 10261-10273
    • Green, D.F.1    Tidor, B.2
  • 38
    • 84986505827 scopus 로고
    • Validation of the general-purpose quanta(R)3.2/ CHARMm(R) force-field
    • Momany FA, Rone R. Validation of the general-purpose quanta(R)3.2/ CHARMm(R) force-field. J Comput Chem 1992;13:888-900.
    • (1992) J Comput Chem , vol.13 , pp. 888-900
    • Momany, F.A.1    Rone, R.2
  • 39
    • 21944443282 scopus 로고    scopus 로고
    • Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties
    • Kangas E, Tidor B. Optimizing electrostatic affinity in ligand-receptor binding: theory, computation, and ligand properties. J Chem Phys 1998;109:7522-7545.
    • (1998) J Chem Phys , vol.109 , pp. 7522-7545
    • Kangas, E.1    Tidor, B.2
  • 40
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for evaluation of computational methods
    • Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput-Aided Mol Des 2008;22:133-139.
    • (2008) J Comput-Aided Mol Des , vol.22 , pp. 133-139
    • Jain, A.N.1    Nicholls, A.2
  • 41
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang R, Lu Y, Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 2003;46:2287-2303.
    • (2003) J Med Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 43
    • 0001442195 scopus 로고
    • Solvation free-energies of amides and amines: Disagreement between free energy calculations and experiment
    • Morgantini PY, Kollman PA. Solvation free-energies of amides and amines: disagreement between free energy calculations and experiment. J Am Chem Soc 1995;117:6057-6063.
    • (1995) J Am Chem Soc , vol.117 , pp. 6057-6063
    • Morgantini, P.Y.1    Kollman, P.A.2
  • 44
    • 0000140870 scopus 로고
    • Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials
    • Ding YB, Bernardo DN, Kroghjespersen K, Levy RM. Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem 1995;99:11575-11583.
    • (1995) J Phys Chem , vol.99 , pp. 11575-11583
    • Ding, Y.B.1    Bernardo, D.N.2    Kroghjespersen, K.3    Levy, R.M.4
  • 45
    • 0037089017 scopus 로고    scopus 로고
    • The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators
    • Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 2002;23:517-529.
    • (2002) J Comput Chem , vol.23 , pp. 517-529
    • Gallicchio, E.1    Zhang, L.Y.2    Levy, R.M.3
  • 46
    • 0033606250 scopus 로고    scopus 로고
    • OPLS all-atom model for amines: Resolution of the amine hydration problem
    • Rizzo RC, Jorgensen WL. OPLS all-atom model for amines: resolution of the amine hydration problem. J Am Chem Soc 1999;121: 4827-4836.
    • (1999) J Am Chem Soc , vol.121 , pp. 4827-4836
    • Rizzo, R.C.1    Jorgensen, W.L.2
  • 48
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 2004;25:1656-1676.
    • (2004) J Comput Chem , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 49
    • 33750899801 scopus 로고    scopus 로고
    • Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial, charge models and optimization of nonpolar contributions
    • Rizzo RC, Aynechi T, Case DA, Kuntz ID. Estimation of absolute free energies of hydration using continuum methods: accuracy of partial, charge models and optimization of nonpolar contributions. J Chem Theory Comput 2006;2:128-139.
    • (2006) J Chem Theory Comput , vol.2 , pp. 128-139
    • Rizzo, R.C.1    Aynechi, T.2    Case, D.A.3    Kuntz, I.D.4
  • 50
    • 0000304948 scopus 로고
    • Accurate first principles calculation of molecular charge-distributions and solvation energies from ab-initio quantum-mechanics and continuum dielectric theory
    • Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Ringnalda M, Goddard WA, Honig B. Accurate first principles calculation of molecular charge-distributions and solvation energies from ab-initio quantum-mechanics and continuum dielectric theory. J Am Chem Soc 1994;116:11875-11882.
    • (1994) J Am Chem Soc , vol.116 , pp. 11875-11882
    • Tannor, D.J.1    Marten, B.2    Murphy, R.3    Friesner, R.A.4    Sitkoff, D.5    Nicholls, A.6    Ringnalda, M.7    Goddard, W.A.8    Honig, B.9
  • 51
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: Towards prediction paradise?
    • van de Waterbeemd H, Gifford E. ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2003;2:192-204.
    • (2003) Nat Rev Drug Discov , vol.2 , pp. 192-204
    • van de Waterbeemd, H.1    Gifford, E.2
  • 52
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins Struct Funct Bioin-form 2005;61:704-721.
    • (2005) Proteins Struct Funct Bioin-form , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 53
    • 33947119575 scopus 로고    scopus 로고
    • Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments
    • Czodrowski P, Sotriffer CA, Klebe G. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pKa calculations and ITC experiments. J Mol Biol 2007; 367:1347-1356.
    • (2007) J Mol Biol , vol.367 , pp. 1347-1356
    • Czodrowski, P.1    Sotriffer, C.A.2    Klebe, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.