메뉴 건너뛰기




Volumn 10, Issue 7, 2015, Pages

An effective approach for clustering InhA molecular dynamics trajectory using substrate-binding cavity features

Author keywords

[No Author keywords available]

Indexed keywords

ENOYL ACYL CARRIER PROTEIN REDUCTASE (NADH); INHA ENZYME; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; INHA PROTEIN, MYCOBACTERIUM; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE;

EID: 84941924740     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0133172     Document Type: Article
Times cited : (21)

References (55)
  • 1
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • PMID: 12198485
    • Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002; 9: 646-652. PMID: 12198485.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 2
    • 80054950510 scopus 로고    scopus 로고
    • Molecular dynamics simulations and drug discovery
    • PMID: 22035460
    • Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. BMC Biol. 2011; 9: 71. doi:10.1186/1741-7007-9-71 PMID: 22035460.
    • (2011) BMC Biol , vol.9 , pp. 71
    • Durrant, J.D.1    McCammon, J.A.2
  • 3
    • 33747200808 scopus 로고    scopus 로고
    • Combining docking and molecular dynamic simulations in drug design
    • PMID: 16758486
    • Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev. 2006; 26: 531-568. PMID: 16758486.
    • (2006) Med Res Rev , vol.26 , pp. 531-568
    • Alonso, H.1    Bliznyuk, A.A.2    Gready, J.E.3
  • 4
    • 78650813408 scopus 로고    scopus 로고
    • Mining flexible-receptor docking experiments to select promising protein receptor snapshots
    • Machado KS, Winck AT, Ruiz DD, Norberto de Souza O. Mining flexible-receptor docking experiments to select promising protein receptor snapshots. BMC Genomics. 2010; 11: 1-10.
    • (2010) BMC Genomics , vol.11 , pp. 1-10
    • Machado, K.S.1    Winck, A.T.2    Ruiz, D.D.3    Norberto De Souza., O.4
  • 6
    • 34548742854 scopus 로고    scopus 로고
    • Chemdb update-full-text search and virtual chemical space
    • PMID: 17599932
    • Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P. ChemDB update-full-text search and virtual chemical space. Bioinformatics. 2007; 23: 2348-2351. PMID: 17599932.
    • (2007) Bioinformatics , vol.23 , pp. 2348-2351
    • Chen, J.H.1    Linstead, E.2    Swamidass, S.J.3    Wang, D.4    Baldi, P.5
  • 8
    • 84869987352 scopus 로고    scopus 로고
    • Enumeration of 166 billion organic small molecules in the chemical universe database gdb-17
    • PMID: 23088335
    • Ruddigkeit L, van Deursen R, Blum LC, Reymond JL. Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. J Chem Inf Model. 2012; 52: 2864-2875. doi:10.1021/ci300415d PMID: 23088335.
    • (2012) J Chem Inf Model , vol.52 , pp. 2864-2875
    • Ruddigkeit, L.1    Van Deursen, R.2    Blum, L.C.3    Reymond, J.L.4
  • 9
    • 77949351042 scopus 로고    scopus 로고
    • Emerging methods for ensemble-based virtual screening
    • Amaro RE, Li WW. Emerging methods for ensemble-based virtual screening. Curr Top Med Chem. 2010; 10: 2-13.
    • (2010) Curr Top Med Chem , vol.10 , pp. 2-13
    • Amaro, R.E.1    Li, W.W.2
  • 10
    • 84904303357 scopus 로고    scopus 로고
    • A strategic solution to optimize molecular docking simulations using fully-flexible receptor models
    • Quevedo CV, De Paris R, Ruiz DD, Norberto de Souza O. A strategic solution to optimize molecular docking simulations using fully-flexible receptor models. Expert Syst Appl. 2014; 41: 7608-7620.
    • (2014) Expert Syst Appl , vol.41 , pp. 7608-7620
    • Quevedo, C.V.1    De Paris, R.2    Ruiz, D.D.3    Norberto De Souza, O.4
  • 11
    • 33746878817 scopus 로고    scopus 로고
    • Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core
    • PMID: 16859306
    • Li Y. Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core. J Chem Inf Model. 2006; 46: 1742-1750. PMID: 16859306.
    • (2006) J Chem Inf Model , vol.46 , pp. 1742-1750
    • Li, Y.1
  • 12
    • 81055148354 scopus 로고    scopus 로고
    • Validating clustering of molecular dynamics simulations using polymer models
    • PMID: 22082218
    • Phillips JL, Colvin ME, Newsam S. Validating clustering of molecular dynamics simulations using polymer models. BMC Bioinformatics. 2011; 12: 445-468doi:10.1186/1471-2105-12-445 PMID: 22082218.
    • (2011) BMC Bioinformatics , vol.12 , pp. 445-468
    • Phillips, J.L.1    Colvin, M.E.2    Newsam, S.3
  • 13
    • 38549150173 scopus 로고    scopus 로고
    • Novel druggable hot spots in avian influenza neuraminidase h5n1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    • PMID: 18205727
    • Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, et al. Novel druggable hot spots in avian influenza neuraminidase h5n1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des. 2008; 71: 106-116. doi:10.1111/j.1747-0285.2007.00614.xPMID: 18205727.
    • (2008) Chem Biol Drug des , vol.71 , pp. 106-116
    • Landon, M.R.1    Amaro, R.E.2    Baron, R.3    Ngan, C.H.4    Ozonoff, D.5    McCammon, J.A.6
  • 14
    • 14944359976 scopus 로고    scopus 로고
    • Dynamic receptor-based pharmacophore model development and its application in designing novel HIV-1 integrase inhibitors
    • PMID: 15743192
    • Deng J, Lee KW, Sanchez T, Cui M, Neamati N, Briggs JM. Dynamic receptor-based pharmacophore model development and its application in designing novel hiv-1 integrase inhibitors. J Med Chem. 2005; 48: 1496-1505. PMID: 15743192.
    • (2005) J Med Chem , vol.48 , pp. 1496-1505
    • Deng, J.1    Lee, K.W.2    Sanchez, T.3    Cui, M.4    Neamati, N.5    Briggs, J.M.6
  • 16
    • 36649006642 scopus 로고    scopus 로고
    • Clusteringmolecular dynamics trajectories: 1.characterizing the performance of different clustering algorithms
    • Shao J, Tanner SW, Thompson N, Cheatham TE. Clusteringmolecular dynamics trajectories: 1.characterizing the performance of different clustering algorithms. J ChemTheory Comput. 2007; 3: 2312-2334.
    • (2007) J ChemTheory Comput , vol.3 , pp. 2312-2334
    • Shao, J.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 17
    • 84986435778 scopus 로고
    • Algorithms for clustering molecular dynamics configurations
    • Torda AE, van Gunsteren WF. Algorithms for clustering molecular dynamics configurations. J Comput Chem. 1994; 15: 1331-1340.
    • (1994) J Comput Chem , vol.15 , pp. 1331-1340
    • Torda, A.E.1    Van Gunsteren, W.F.2
  • 19
    • 0029152775 scopus 로고
    • Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
    • Troyer JM, Cohen FE. Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory. Proteins: Struct, Funct, Bioinf. 1995; 23: 97-110.
    • (1995) Proteins: Struct, Funct, Bioinf , vol.23 , pp. 97-110
    • Troyer, J.M.1    Cohen, F.E.2
  • 21
    • 84972893020 scopus 로고
    • A dendrite method for cluster analysis
    • Calinski T, Harabasz J. A dendrite method for cluster analysis. Commun Stat A-Theor. 1974; 3: 1-27.
    • (1974) Commun Stat A-Theor , vol.3 , pp. 1-27
    • Calinski, T.1    Harabasz, J.2
  • 22
    • 33745759471 scopus 로고    scopus 로고
    • Ensemble-based convergence analysis of biomolecular trajectories
    • PMID: 16617086
    • Lyman E, Zuckerman DM. Ensemble-based convergence analysis of biomolecular trajectories. Biophys J. 2006; 91: 164-172. PMID: 16617086.
    • (2006) Biophys J , vol.91 , pp. 164-172
    • Lyman, E.1    Zuckerman, D.M.2
  • 23
    • 70349932423 scopus 로고    scopus 로고
    • Autodock4 and autodock- tools4: Automated docking with selective receptor flexibility
    • PMID: 19399780
    • Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsel DS, et al. AutoDock4 and AutoDock- Tools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30: 2785-2791. doi:10.1002/jcc.21256 PMID: 19399780.
    • (2009) J Comput Chem , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3    Sanner, M.F.4    Belew, R.K.5    Goodsel, D.S.6
  • 26
    • 0028988237 scopus 로고
    • Crystal structure and function of the isoniazid target of mycobacterium tuberculosis
    • Dessen A, Quemard A, Blanchard JS, Jacobs WR, Sacchettini JC. Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science. 1995; 267:1638-1641.
    • (1995) Science , vol.267 , pp. 1638-1641
    • Dessen, A.1    Quemard, A.2    Blanchard, J.S.3    Jacobs, W.R.4    Sacchettini, J.C.5
  • 30
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
    • van Gunsteren WF, Berendsen HJ. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry. Angew Chem Int Ed Engl. 1990; 29: 992-1023.
    • (1990) Angew Chem Int Ed Engl , vol.29 , pp. 992-1023
    • Van Gunsteren, W.F.1    Berendsen, H.J.2
  • 31
    • 0028815118 scopus 로고
    • Molecular dynamic simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion
    • PMID: 7716168
    • Ryde U. Molecular dynamic simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins. 1995; 21: 40-56. PMID: 7716168.
    • (1995) Proteins , vol.21 , pp. 40-56
    • Ryde, U.1
  • 32
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges-the resp model
    • Bayly CI, Cielplak 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    Cielplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 33
    • 1942519275 scopus 로고    scopus 로고
    • Spicker: A clustering approach to identify near-native protein folds
    • PMID: 15011258
    • Zhang Y, Skolnick J. Spicker: A clustering approach to identify near-native protein folds. J Comput Chem. 2004; 25: 865-871. PMID: 15011258.
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 34
    • 55849113760 scopus 로고    scopus 로고
    • Cavity clustering based on community structure of pocket similarity network
    • Protein, PMID: 19008186
    • Liu ZP, Wu LY, Wang Y, Zhang XS. Protein cavity clustering based on community structure of pocket similarity network. Int J Bioinform Res Appl. 2008; 4: 445-460. PMID: 19008186.
    • (2008) Int J Bioinform Res Appl , vol.4 , pp. 445-460
    • Liu, Z.P.1    Wu, L.Y.2    Wang, Y.3    Zhang, X.S.4
  • 35
    • 0040017633 scopus 로고    scopus 로고
    • Crystal structure of the mycobacterium tuberculosis enoyl-acp reductase, inha, in complex with nad+ and a c16 fatty acyl substrate
    • PMID: 10336454
    • Rozwarski DA, Vilchèze C, Sugantino M, Bittman R, Sacchettini JC. Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate. J Biol Chem. 1999; 274: 15582-15589. PMID: 10336454.
    • (1999) J Biol Chem , vol.274 , pp. 15582-15589
    • Rozwarski, D.A.1    Vilchèze, C.2    Sugantino, M.3    Bittman, R.4    Sacchettini, J.C.5
  • 37
    • 0041989751 scopus 로고    scopus 로고
    • Castp: Computed atlas of surface topography of proteins
    • Binkowski TA, Naghibzadeh S, Liang J. CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res. 2006; 31: 3352-3355.
    • (2006) Nucleic Acids Res , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1    Naghibzadeh, S.2    Liang, J.3
  • 39
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biophys Bio. 1977; 6:151-176.
    • (1977) Annu Rev Biophys Bio , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 40
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML. Analytical molecular surface calculation. J Appl Crystallogr. 1983; 16: 548-558.
    • (1983) J Appl Crystallogr , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 41
    • 84965102247 scopus 로고    scopus 로고
    • Team RC R:, R Foundation for Statistical Computing, Vienna, Austria, Technical report
    • Team RC R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2012. Technical report.
    • (2012) A Language and Environment for Statistical Computing
  • 47
    • 84884567429 scopus 로고    scopus 로고
    • Discovery of new inhibitors of mycobacterium tuberculosis inha enzyme using virtual screening and a 3d-pharmacophore- based approach
    • PMID: 23889525
    • Pauli I, Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LFSM, et al. Discovery of New Inhibitors of Mycobacterium tuberculosis InhA Enzyme Using Virtual Screening and a 3D-Pharmacophore- Based Approach. J Chem Inf Model. 2013, 53: 2390-2401. doi:10.1021/ci400202t PMID: 23889525.
    • (2013) J Chem Inf Model , vol.53 , pp. 2390-2401
    • Pauli, I.1    Santos, R.N.2    Rostirolla, D.C.3    Martinelli, L.K.4    Ducati, R.G.5    Timmers, L.F.S.M.6
  • 48
    • 84877277360 scopus 로고    scopus 로고
    • Wfredow: A cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model
    • De Paris R, Frantz FA, Norberto de Souza O, Ruiz DD. wFReDoW: A cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model. BioMed Res. 2013; 2013:1-12.
    • (2013) BioMed Res , vol.2013 , pp. 1-12
    • De Paris, R.1    Frantz, F.A.2    Norberto, D.S.O.3    Ruiz, D.D.4
  • 49
    • 49449088906 scopus 로고    scopus 로고
    • Identification and validation of human DNA ligase inhibitors using computer-aided drug design
    • PMID: 18630893
    • Zhong S, Chen X, Zhu X, Dziegielewska B, Bachman KE, Ellenberger T, et al. Identification and validation of human dna ligase inhibitors using computer-aided drug design. J Med Chem. 2008; 51: 4553-4562. doi:10.1021/jm8001668 PMID: 18630893.
    • (2008) J Med Chem , vol.51 , pp. 4553-4562
    • Zhong, S.1    Chen, X.2    Zhu, X.3    Dziegielewska, B.4    Bachman, K.E.5    Ellenberger, T.6
  • 50
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • PMID: 18558668
    • Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem. 2008; 51: 3878-3894. doi:10.1021/jm8001197 PMID: 18558668.
    • (2008) J Med Chem , vol.51 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 51
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • PMID: 10623530
    • Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol. 2000; 295: 337-356. PMID: 10623530.
    • (2000) J Mol Biol , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 52
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • PMID: 18302984
    • Totrov M, Abagyan R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr Opin Struct Biol. 2008; 18: 178-184. doi:10.1016/j.sbi.2008.01.004 PMID: 18302984.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.