메뉴 건너뛰기




Volumn 17, Issue 8, 2011, Pages 1919-1926

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation

Author keywords

Binding free energy; MM GBSA; Molecular dynamics simulation; ScFv

Indexed keywords

ADENOSINE PHOSPHATE; AMPHETAMINE; METHAMPHETAMINE; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY;

EID: 80051791940     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0892-4     Document Type: Article
Times cited : (12)

References (31)
  • 1
    • 80051782845 scopus 로고    scopus 로고
    • NDIC (2008) Johnstown, PA: National drug intelligence center
    • NDIC (2008) Johnstown, PA: National drug intelligence center
  • 2
    • 22444437907 scopus 로고    scopus 로고
    • Vaccine pharmacotherapy for the treatment of cocaine dependence
    • DOI 10.1016/j.biopsych.2005.04.032, PII S0006322305004932
    • BA Martell E Mitchell J Poling K Gonsai TR Kosten 2005 Biol Psychiatry 58 158 164 10.1016/j.biopsych.2005.04.032 1:CAS:528:DC%2BD2MXmsVWrsLs%3D (Pubitemid 41008133)
    • (2005) Biological Psychiatry , vol.58 , Issue.2 , pp. 158-164
    • Martell, B.A.1    Mitchell, E.2    Poling, J.3    Gonsai, K.4    Kosten, T.R.5
  • 6
    • 0034979318 scopus 로고    scopus 로고
    • Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
    • DOI 10.1146/annurev.biophys.30.1.211
    • W Wang O Donini CM Reyes PA Kollman 2001 Annu Rev Biophys Biomol Struct 30 211 243 10.1146/annurev.biophys.30.1.211 1:CAS:528:DC%2BD3MXkvVaqsbY%3D (Pubitemid 32566163)
    • (2001) Annual Review of Biophysics and Biomolecular Structure , vol.30 , pp. 211-243
    • Wang, W.1    Donini, O.2    Reyes, C.M.3    Kollman, P.A.4
  • 8
    • 0029757992 scopus 로고    scopus 로고
    • 10.1016/S0006-3495(96)79267-6 1:CAS:528:DyaK28XkslOqtb4%3D
    • B Roux M Nina R Pomès JC Smith 1996 Biophys J 71 670 681 10.1016/S0006-3495(96)79267-6 1:CAS:528:DyaK28XkslOqtb4%3D
    • (1996) Biophys J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomès, R.3    Smith, J.C.4
  • 9
    • 54949149944 scopus 로고    scopus 로고
    • 10.1063/1.2992153 1:STN:280:DC%2BD1cjnslOkuw%3D%3D
    • LY Chen 2008 J Chem Phys 129 144113 144117 10.1063/1.2992153 1:STN:280:DC%2BD1cjnslOkuw%3D%3D
    • (2008) J Chem Phys , vol.129 , pp. 144113-144117
    • Chen, L.Y.1
  • 11
    • 39749152456 scopus 로고    scopus 로고
    • Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    • DOI 10.1021/ja0779250
    • I Stoica SK Sadiq PV Coveney 2008 J Am Chem Soc 130 2639 2648 10.1021/ja0779250 1:CAS:528:DC%2BD1cXhtFShtb0%3D (Pubitemid 351304779)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.8 , pp. 2639-2648
    • Stoica, I.1    Sadiq, S.K.2    Coveney, P.V.3
  • 12
    • 33947644064 scopus 로고    scopus 로고
    • Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance
    • DOI 10.1021/jm0609162
    • TJ Hou R Yu 2007 J Med Chem 50 1177 1188 10.1021/jm0609162 1:CAS:528:DC%2BD2sXhs1Ghtbk%3D (Pubitemid 46496318)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.6 , pp. 1177-1188
    • Hou, T.1    Yu, R.2
  • 15
    • 77955653070 scopus 로고    scopus 로고
    • 10.1007/s10822-010-9366-0 1:CAS:528:DC%2BC3cXos1ylurw%3D
    • G Hu D Wang X Liu Q Zhang 2010 J Comput Aided Mol Des 24 687 697 10.1007/s10822-010-9366-0 1:CAS:528:DC%2BC3cXos1ylurw%3D
    • (2010) J Comput Aided Mol des , vol.24 , pp. 687-697
    • Hu, G.1    Wang, D.2    Liu, X.3    Zhang, Q.4
  • 16
    • 53849113368 scopus 로고    scopus 로고
    • 10.1002/chem.200800277 1:CAS:528:DC%2BD1cXht1OltrnP
    • EL Wu KL Han JZH Zhang 2008 Chem Eur J 14 8704 8714 10.1002/chem. 200800277 1:CAS:528:DC%2BD1cXht1OltrnP
    • (2008) Chem Eur J , vol.14 , pp. 8704-8714
    • Wu, E.L.1    Han, K.L.2    Zhang, J.Z.H.3
  • 17
    • 68949194753 scopus 로고    scopus 로고
    • 10.1007/s00894-009-0452-y 1:CAS:528:DC%2BC3cXlslGjtLg%3D
    • J Chen M Yang G Hu S Shi C Yi Q Zhang 2009 J Mol Model 15 1245 1252 10.1007/s00894-009-0452-y 1:CAS:528:DC%2BC3cXlslGjtLg%3D
    • (2009) J Mol Model , vol.15 , pp. 1245-1252
    • Chen, J.1    Yang, M.2    Hu, G.3    Shi, S.4    Yi, C.5    Zhang, Q.6
  • 18
    • 20644449471 scopus 로고    scopus 로고
    • 10.1021/jp994072s 1:CAS:528:DC%2BD3cXhvVGit70%3D
    • A Onufriev D Bashford DA Case 2000 J Phys Chem B 104 3712 3720 10.1021/jp994072s 1:CAS:528:DC%2BD3cXhvVGit70%3D
    • (2000) J Phys Chem B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 19
    • 33746686285 scopus 로고    scopus 로고
    • Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase
    • DOI 10.1021/jm060222t
    • SB Rafi G Cui K Song X Cheng PJ Tonge C Simmerling 2006 J Med Chem 49 4574 4580 10.1021/jm060222t 1:CAS:528:DC%2BD28Xms1SltL4%3D (Pubitemid 44162683)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.15 , pp. 4574-4580
    • Rafi, S.B.1    Cui, G.2    Song, K.3    Cheng, X.4    Tonge, P.J.5    Simmerling, C.6
  • 21
    • 80051789416 scopus 로고    scopus 로고
    • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani 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 (2004) Gaussian Inc, Wallingford, CT
    • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani 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 (2004) Gaussian Inc, Wallingford, CT
  • 24
    • 0034602373 scopus 로고    scopus 로고
    • 10.1006/jmbi.2000.4057 1:CAS:528:DC%2BD3cXotlyit7k%3D
    • W Wang PA Kollman 2000 J Mol Biol 303 567 582 10.1006/jmbi.2000.4057 1:CAS:528:DC%2BD3cXotlyit7k%3D
    • (2000) J Mol Biol , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.A.2
  • 26
    • 80051793569 scopus 로고    scopus 로고
    • Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) University of California, San Francisco
    • Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) University of California, San Francisco
  • 27
  • 29
    • 0032558981 scopus 로고    scopus 로고
    • Structure-based design of potent inhibitors of scytalone dehydratase: Displacement of a water molecule from the active site
    • DOI 10.1021/bi981848r
    • JM Chen SL Xu Z Wawrzak GS Basarab DB Jordan 1998 Biochemistry 37 17735 17744 10.1021/bi981848r 1:CAS:528:DyaK1cXns1ahur8%3D (Pubitemid 29023928)
    • (1998) Biochemistry , vol.37 , Issue.51 , pp. 17735-17744
    • Chen, J.M.1    Xu, S.L.2    Wawrzak, Z.3    Basarab, G.S.4    Jordan, D.B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.