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Volumn , Issue , 2015, Pages 195-219

In silico design of antimicrobial peptides

Author keywords

Amps; De novo peptide design; Drug resistance; Molecular dynamics; Qsar

Indexed keywords

DRUG THERAPY; MICROORGANISMS; MOLECULAR DYNAMICS; MOLECULES; POLYPEPTIDES;

EID: 84921820136     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4939-2285-7_9     Document Type: Chapter
Times cited : (9)

References (70)
  • 1
    • 84908200723 scopus 로고    scopus 로고
    • Treatment of microbial biofilms in the post antibiotic era: prophylactic and therapeutic use of antimicrobial peptides and their design by bioinformatics tools
    • Accessed 14 Feb 2014
    • Di Luca M, Maccari G, Nifosì R (2014) Treatment of microbial biofilms in the post antibiotic era: prophylactic and therapeutic use of antimicrobial peptides and their design by bioinformatics tools. Pathog Dis. http://www. ncbi.nlm.nih.gov/pubmed/24515391. Accessed 14 Feb 2014
    • (2014) Pathog Dis
    • Di Luca, M.1    Maccari, G.2    Nifosì, R.3
  • 2
    • 84880797054 scopus 로고    scopus 로고
    • In vitro efficient transfection by CM18-Tat11 hybrid peptide: a new tool for gene-delivery applications
    • Salomone F, Cardarelli F, Signore G, Boccardi C, Beltram F (2013) In vitro efficient transfection by CM18-Tat11 hybrid peptide: a new tool for gene-delivery applications. PLoS One. doi:10.1371/journal.pone.0070108
    • (2013) PLoS One
    • Salomone, F.1    Cardarelli, F.2    Signore, G.3    Boccardi, C.4    Beltram, F.5
  • 3
    • 84888632051 scopus 로고    scopus 로고
    • Antimicrobial peptides
    • Accessed 29 Nov 2013
    • Bahar A, Ren D (2013) Antimicrobial peptides. Pharmaceuticals 6:1543-1575. http://www.mdpi.com/1424-8247/6/12/1543/. Accessed 29 Nov 2013
    • (2013) Pharmaceuticals , vol.6 , pp. 1543-1575
    • Bahar, A.1    Ren, D.2
  • 4
    • 0034824597 scopus 로고    scopus 로고
    • From "carpet" mechanism to de-novo designed diastereomeric cell-selective antimicrobial peptides
    • Accessed 29 Dec 2012
    • Shai Y, Oren Z (2001) From "carpet" mechanism to de-novo designed diastereomeric cell-selective antimicrobial peptides. Peptides 22:1629-1641. http://www.ncbi.nlm.nih.gov/pubmed/11587791. Accessed 29 Dec 2012
    • (2001) Peptides , vol.22 , pp. 1629-1641
    • Shai, Y.1    Oren, Z.2
  • 5
    • 34249858459 scopus 로고    scopus 로고
    • AMPer: a database and an automated discovery tool for antimicrobial peptides
    • Accessed 10 May 2013
    • Fjell CD, Hancock REW, Cherkasov A (2007) AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23:1148-1155. http://www.ncbi.nlm.nih.gov/pubmed/17341497. Accessed 10 May 2013
    • (2007) Bioinformatics , vol.23 , pp. 1148-1155
    • Fjell, C.D.1    Hancock, R.E.W.2    Cherkasov, A.3
  • 6
    • 48249157851 scopus 로고    scopus 로고
    • Biomolecular engineering by combinatorial design and high-throughput screening: small, soluble peptides that permeabilize membranes
    • Accessed 22 May 2013
    • Rathinakumar R, Wimley WC (2008) Biomolecular engineering by combinatorial design and high-throughput screening: small, soluble peptides that permeabilize membranes. J Am Chem Soc 130:9849-9858. http://www.pub medcentral.nih.gov/articlerender.fcgi?artid=2582735&tool=pmcentrez&rendertype=abstr act. Accessed 22 May 2013
    • (2008) J Am Chem Soc , vol.130 , pp. 9849-9858
    • Rathinakumar, R.1    Wimley, W.C.2
  • 7
    • 79958796013 scopus 로고    scopus 로고
    • Spontaneous membrane-translocating peptides by orthogonal high-throughput screening
    • Accessed 3 Jan 2013
    • Marks JR, Placone J, Hristova K, Wimley WC (2011) Spontaneous membrane-translocating peptides by orthogonal high-throughput screening. J Am Chem Soc 133:8995-9004. http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=3118567&tool=pmcentrez&rendertype= abstract. Accessed 3 Jan 2013
    • (2011) J Am Chem Soc , vol.133 , pp. 8995-9004
    • Marks, J.R.1    Placone, J.2    Hristova, K.3    Wimley, W.C.4
  • 8
    • 79954616130 scopus 로고    scopus 로고
    • Prediction of antimicrobial peptides based on sequence alignment and feature selection methods
    • Accessed 15 Mar 2012
    • Wang P, Hu L, Liu G, Jiang N, Chen X et al (2011) Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS One 6: e18476. http://www.pubmedcentral.nih.gov/articlerender.fcg i?artid=3076375&tool=pmcentrez&rendertyp e=abstract. Accessed 15 Mar 2012
    • (2011) PLoS One , vol.6 , pp. e18476
    • Wang, P.1    Hu, L.2    Liu, G.3    Jiang, N.4    Chen, X.5
  • 9
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • Accessed 21 Jan 2014
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29. http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=3037419&tool=pmcentrez&render type=abstract. Accessed 21 Jan 2014
    • (2000) The Gene Ontology Consortium. Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 10
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Accessed 30 July 2012
    • Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659. http://www.ncbi.nlm.nih.gov/pubmed/16731699. Accessed 30 July 2012
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 11
    • 84858277472 scopus 로고    scopus 로고
    • YADAMP: yet another database of antimicrobial peptides
    • Piotto SP, Sessa L, Concilio S, Iannelli P (2012) YADAMP: yet another database of antimicrobial peptides. Int J Antimicrob Agents 39:346-351. http://www.ncbi.nlm. nih.gov/pubmed/22325123. Accessed 23 Aug 2012
    • (2012) Int J Antimicrob Agents , vol.39 , pp. 346-351
    • Piotto, S.P.1    Sessa, L.2    Concilio, S.3    Iannelli, P.4
  • 12
    • 75549090102 scopus 로고    scopus 로고
    • CAMP: a useful resource for research on antimicrobial peptides
    • Accessed 23 Aug 2012
    • Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38: D774-D780. http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=2808926&tool=pmcentrez& rendertype=abstract. Accessed 23 Aug 2012
    • (2010) Nucleic Acids Res , vol.38 , pp. D774-D780
    • Thomas, S.1    Karnik, S.2    Barai, R.S.3    Jayaraman, V.K.4    Idicula-Thomas, S.5
  • 13
    • 0027215340 scopus 로고
    • DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures
    • Accessed 23 July 2012
    • Wold S, Jonsson J, Sjörström M, Sandberg M, Rännar S (1993) DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures. Anal Chim Acta 277:239-253. http://linkinghub.elsevier.com/retrieve/pii/000326709380437P. Accessed 23 July 2012
    • (1993) Anal Chim Acta , vol.277 , pp. 239-253
    • Wold, S.1    Jonsson, J.2    Sjörström, M.3    Sandberg, M.4    Rännar, S.5
  • 14
    • 29244463544 scopus 로고    scopus 로고
    • Population structure inferred by local spatial autocorrelation:an example from an Amerindian tribal population
    • Accessed 13 Feb 2014
    • Sokal RR, Thomson BA (2006) Population structure inferred by local spatial autocorrelation:an example from an Amerindian tribal population. Am J Phys Anthropol 129:121-131. http://www.ncbi.nlm.nih.gov/pubmed/16261547. Accessed 13 Feb 2014
    • (2006) Am J Phys Anthropol , vol.129 , pp. 121-131
    • Sokal, R.R.1    Thomson, B.A.2
  • 15
    • 0023972269 scopus 로고
    • Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities
    • Accessed 13 Feb 2014
    • Horne DS (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers 27:451-477. http://www.ncbi.nlm.nih.gov/pubmed/3359010. Accessed 13 Feb 2014
    • (1988) Biopolymers , vol.27 , pp. 451-477
    • Horne, D.S.1
  • 16
    • 0033781978 scopus 로고    scopus 로고
    • Prediction of membrane protein types based on the hydrophobic index of amino acids
    • Accessed 13 Feb 2014
    • Feng ZP, Zhang CT (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. J Protein Chem 19:269-275. http://www.ncbi.nlm.nih.gov/pubmed/11043931. Accessed 13 Feb 2014
    • (2000) J Protein Chem , vol.19 , pp. 269-275
    • Feng, Z.P.1    Zhang, C.T.2
  • 17
    • 80051725174 scopus 로고    scopus 로고
    • Distinguishing compounds with anticancer activity by ANN using inductive QSAR descriptors
    • Accessed 13 Feb 2014
    • Jaiswal K, Naik PK (2008) Distinguishing compounds with anticancer activity by ANN using inductive QSAR descriptors. Bioinformation 2:441-451. http://www.pubmedcentral.nih. gov/articlerender.fcgi?artid=2561164&tool= pmcentrez&rendertype=abstract. Accessed 13 Feb 2014
    • (2008) Bioinformation , vol.2 , pp. 441-451
    • Jaiswal, K.1    Naik, P.K.2
  • 18
    • 84864457002 scopus 로고    scopus 로고
    • forestSV: structural variant discovery through statistical learning
    • Accessed 24 Aug 2012
    • Michaelson JJ, Sebat J (2012) forestSV: structural variant discovery through statistical learning. Nat Methods 9:819-821. http://www. ncbi.nlm.nih.gov/pubmed/22751202. Accessed 24 Aug 2012
    • (2012) Nat Methods , vol.9 , pp. 819-821
    • Michaelson, J.J.1    Sebat, J.2
  • 19
    • 84879140552 scopus 로고    scopus 로고
    • Data mining in the life sciences with random forest: a walk in the park or lost in the jungle?
    • Accessed 17 July 2012
    • Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J et al (2012) Data mining in the life sciences with random forest: a walk in the park or lost in the jungle? Brief Bioinform. http://www.ncbi.nlm.nih.gov/pubmed/22786785. Accessed 17 July 2012
    • (2012) Brief Bioinform
    • Touw, W.G.1    Bayjanov, J.R.2    Overmars, L.3    Backus, L.4    Boekhorst, J.5
  • 20
    • 84884689688 scopus 로고    scopus 로고
    • Antimicrobial peptides design by evolutionary multiobjective optimization
    • Accessed 23 Sept 2013
    • Maccari G, Di Luca M, Nifosí R, Cardarelli F, Signore G, et al (2013) Antimicrobial peptides design by evolutionary multiobjective optimization. PLoS Comput Biol 9: e1003212. http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.1003212. Accessed 23 Sept 2013
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003212
    • Maccari, G.1    Di Luca, M.2    Nifosí, R.3    Cardarelli, F.4    Signore, G.5
  • 21
    • 66849131414 scopus 로고    scopus 로고
    • Controlling feature selection in random forests of decision trees using a genetic algorithm: classification of class I MHC peptides
    • Accessed 14 Feb 2014
    • Hansen L, Lee EA, Hestir K, Williams LT, Farrelly D (2009) Controlling feature selection in random forests of decision trees using a genetic algorithm: classification of class I MHC peptides. Comb Chem High Throughput Screen 12: 514-519. http://www.ncbi. nlm.nih.gov/pubmed/19519331. Accessed 14 Feb 2014
    • (2009) Comb Chem High Throughput Screen , vol.12 , pp. 514-519
    • Hansen, L.1    Lee, E.A.2    Hestir, K.3    Williams, L.T.4    Farrelly, D.5
  • 22
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy
    • Accessed 23 July 2012
    • Peng H, Long F, Ding C (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell27 27:1226-1238. http://www.ncbi.nlm. nih.gov/pubmed/16119262. Accessed 23 July 2012
    • (2005) IEEE Trans Pattern Anal Mach Intell27 , vol.27 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 23
    • 34047232962 scopus 로고    scopus 로고
    • Design of MHC I stabilizing peptides by agent-based exploration of sequence space
    • Accessed 14 Feb 2014
    • Hiss JA, Bredenbeck A, Losch FO, Wrede P, Walden P et al (2007) Design of MHC I stabilizing peptides by agent-based exploration of sequence space. Protein Eng Des Sel 20:99-108. http://www.ncbi.nlm.nih.gov/pubmed/17314106. Accessed 14 Feb 2014
    • (2007) Protein Eng Des Sel , vol.20 , pp. 99-108
    • Hiss, J.A.1    Bredenbeck, A.2    Losch, F.O.3    Wrede, P.4    Walden, P.5
  • 24
    • 78650156321 scopus 로고    scopus 로고
    • Optimization of antibacterial peptides by genetic algorithms and cheminformatics
    • Accessed 25 May 2012
    • Fjell CD, Jenssen H, Cheung WA, Hancock REW, Cherkasov A (2011) Optimization of antibacterial peptides by genetic algorithms and cheminformatics. Chem Biol Drug Des 77:48-56. http://www.ncbi.nlm.nih.gov/pubmed/20942839. Accessed 25 May 2012
    • (2011) Chem Biol Drug Des , vol.77 , pp. 48-56
    • Fjell, C.D.1    Jenssen, H.2    Cheung, W.A.3    Hancock, R.E.W.4    Cherkasov, A.5
  • 25
    • 0036530772 scopus 로고    scopus 로고
    • A fast and elitist multiobjective genetic algorithm: NSGA-II
    • Accessed 14 July 2012
    • Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans Evol Comput 6:182-197. http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=996017. Accessed 14 July 2012
    • (2002) IEEE Trans Evol Comput , vol.6 , pp. 182-197
    • Deb, K.1    Pratap, A.2    Agarwal, S.3    Meyarivan, T.4
  • 26
    • 79960953216 scopus 로고    scopus 로고
    • Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides
    • Accessed 6 Aug 2013
    • Bocchinfuso G, Bobone S, Mazzuca C, Palleschi A, Stella L (2011) Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides. Cell Mol Life Sci 68:2281-2301. http://www. ncbi.nlm.nih.gov/pubmed/21584808. Accessed 6 Aug 2013
    • (2011) Cell Mol Life Sci , vol.68 , pp. 2281-2301
    • Bocchinfuso, G.1    Bobone, S.2    Mazzuca, C.3    Palleschi, A.4    Stella, L.5
  • 27
    • 77958066477 scopus 로고    scopus 로고
    • Defect-mediated trafficking across cell membranes: insights from in silico modeling
    • Accessed 7 Aug 2013
    • Gurtovenko AA, Anwar J, Vattulainen I (2010) Defect-mediated trafficking across cell membranes: insights from in silico modeling. Chem Rev 110: 6077-6103. http://www. ncbi.nlm.nih.gov/pubmed/20690701. Accessed 7 Aug 2013
    • (2010) Chem Rev , vol.110 , pp. 6077-6103
    • Gurtovenko, A.A.1    Anwar, J.2    Vattulainen, I.3
  • 28
    • 58149181485 scopus 로고    scopus 로고
    • Lipids on the move: simulations of membrane pores, domains, stalks and curves
    • Accessed 7 Aug 2013
    • Marrink SJ, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta 1788:149-168. http://www. ncbi.nlm.nih.gov/pubmed/19013128. Accessed 7 Aug 2013
    • (2009) Biochim Biophys Acta , vol.1788 , pp. 149-168
    • Marrink, S.J.1    de Vries, A.H.2    Tieleman, D.P.3
  • 29
    • 78650521954 scopus 로고    scopus 로고
    • Computational studies of protegrin antimicrobial peptides: a review
    • Accessed 7 Aug 2013
    • Bolintineanu DS, Kaznessis YN (2011) Computational studies of protegrin antimicrobial peptides: a review. Peptides 32:188-201. http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=3013618&tool=pmcentrez& rendertype=abstract. Accessed 7 Aug 2013
    • (2011) Peptides , vol.32 , pp. 188-201
    • Bolintineanu, D.S.1    Kaznessis, Y.N.2
  • 30
    • 84855171050 scopus 로고    scopus 로고
    • How the antimicrobial peptides kill bacteria: computational physics insights
    • Accessed 7 Aug 2013
    • Chen L, Gao L (2012) How the antimicrobial peptides kill bacteria: computational physics insights. Commun Comput Phys. http://www.global-sci.com/issue/abstract/readabs. php?vol=11&page=709&issue=3&ppage=725&year=2012. Accessed 7 Aug 2013
    • (2012) Commun Comput Phys
    • Chen, L.1    Gao, L.2
  • 32
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Daggett V (ed), Academic, New York
    • Ponder JW, Case DA (2003) Force fields for protein simulations. In: Daggett V (ed) Protein simulations, vol 66. Academic, New York, pp 27-85. doi:10.1016/S0065-3233(03)66002-X
    • (2003) Protein simulations, vol 66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 33
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: overview and issues
    • Mackerell AD (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25:1584-1604. doi:10.1002/jcc.20082
    • (2004) J Comput Chem , vol.25 , pp. 1584-1604
    • Mackerell, A.D.1
  • 34
    • 77955135754 scopus 로고    scopus 로고
    • Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
    • Lange OF, van der Spoel D, de Groot BL (2010) Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J 99:647-655. doi:10.1016/j.bpj.2010.04.062
    • (2010) Biophys J , vol.99 , pp. 647-655
    • Lange, O.F.1    van der Spoel, D.2    de Groot, B.L.3
  • 35
    • 84857463877 scopus 로고    scopus 로고
    • Systematic validation of protein force fields against experimental data
    • Accessed 21 May 2013
    • Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO et al (2012) Systematic validation of protein force fields against experimental data. PLoS One 7: e32131. http://dx.plos.org/10.1371/journal.pone.0032131. Accessed 21 May 2013
    • (2012) PLoS One , vol.7 , pp. e32131
    • Lindorff-Larsen, K.1    Maragakis, P.2    Piana, S.3    Eastwood, M.P.4    Dror, R.O.5
  • 36
    • 84859611714 scopus 로고    scopus 로고
    • Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
    • Beauchamp KA, Lin Y-S, Das R, Pande VS (2012) Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J Chem Theory Comp 8:1409-1414. doi:10.1021/ct2007814
    • (2012) J Chem Theory Comp , vol.8 , pp. 1409-1414
    • Beauchamp, K.A.1    Lin, Y.-S.2    Das, R.3    Pande, V.S.4
  • 37
    • 84865088597 scopus 로고    scopus 로고
    • Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations
    • Cino EA, Choy W-Y, Karttunen M (2012) Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations. J Chem Theory Comp 8:2725-2740. doi:10.1021/ct300323g
    • (2012) J Chem Theory Comp , vol.8 , pp. 2725-2740
    • Cino, E.A.1    Choy, W.-Y.2    Karttunen, M.3
  • 38
    • 84869067020 scopus 로고    scopus 로고
    • Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study
    • Piggot TJ, Piñeiro Á, Khalid S (2012) Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study. J Chem Theory Comp 8:4593-4609. doi:10.1021/ct3003157
    • (2012) J Chem Theory Comp , vol.8 , pp. 4593-4609
    • Piggot, T.J.1    Á, P.2    Khalid, S.3
  • 39
    • 84865101970 scopus 로고    scopus 로고
    • An extension and further validation of an all-atomistic force field for biological membranes
    • Jämbeck JPM, Lyubartsev AP (2012) An extension and further validation of an all-atomistic force field for biological membranes. J Chem Theory Comp 8:2938-2948. doi:10.1021/ct300342n
    • (2012) J Chem Theory Comp , vol.8 , pp. 2938-2948
    • Jämbeck, J.P.M.1    Lyubartsev, A.P.2
  • 40
    • 84884194561 scopus 로고    scopus 로고
    • The polarizable atomic multipole-based AMOEBA force field for proteins
    • Shi Y, Xia Z, Zhang J, Best R, Wu C et al (2013) The polarizable atomic multipole-based AMOEBA force field for proteins. J Chem Theory Comp 9:4046-4063. doi:10.1021/ct4003702
    • (2013) J Chem Theory Comp , vol.9 , pp. 4046-4063
    • Shi, Y.1    Xia, Z.2    Zhang, J.3    Best, R.4    Wu, C.5
  • 42
    • 0035974484 scopus 로고    scopus 로고
    • Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation:aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/
    • Cieplak P, Caldwell J, Kollman P (2001) Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation:aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/. J Comput Chem 22:1048-1057. doi:10.1002/jcc.1065
    • (2001) J Comput Chem , vol.22 , pp. 1048-1057
    • Cieplak, P.1    Caldwell, J.2    Kollman, P.3
  • 43
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Accessed 3 June 2013
    • Tozzini V (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15:144-150. http://www.ncbi.nlm.nih.gov/pubmed/15837171. Accessed 3 June 2013
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 44
    • 84888825453 scopus 로고    scopus 로고
    • Coarse-grain modelling of protein-protein interactions
    • Baaden M, Marrink SJ (2013) Coarse-grain modelling of protein-protein interactions. Curr Opin Struct Biol 23:878-886. doi:10.1016/j. sbi.2013.09.004
    • (2013) Curr Opin Struct Biol , vol.23 , pp. 878-886
    • Baaden, M.1    Marrink, S.J.2
  • 46
    • 80052804796 scopus 로고    scopus 로고
    • Water defect and pore formation in atomistic and coarse-grained lipid membranes: pushing the limits of coarse graining
    • Bennett WFD, Tieleman DP (2011) Water defect and pore formation in atomistic and coarse-grained lipid membranes: pushing the limits of coarse graining. J Chem Theory Comp 12:2981-2988
    • (2011) J Chem Theory Comp , vol.12 , pp. 2981-2988
    • Bennett, W.F.D.1    Tieleman, D.P.2
  • 47
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems:in serial and in parallel
    • Ayton GS, Noid WG, Voth GA (2007) Multiscale modeling of biomolecular systems:in serial and in parallel. Curr Opin Struct Biol 17:192-198. doi:10.1016/j.sbi.2007.03.004
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 48
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J Comput Phys 23:187-199. doi:10.1016/0021-9991(77)90121-8
    • (1977) J Comput Phys , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 49
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B (1995) The calculation of the potential of mean force using computer simulations. Comput Phys Commun 91:275-282. doi:10.1016/0010-4655(95)00053-I
    • (1995) Comput Phys Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 50
    • 0036790894 scopus 로고    scopus 로고
    • Escaping free-energy minima
    • Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci U S A 99:12562-12566. doi:10.1073/pnas.202427399
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 12562-12566
    • Laio, A.1    Parrinello, M.2
  • 51
    • 0028710015 scopus 로고
    • Local elevation: a method for improving the searching properties of molecular dynamics simulation
    • Huber T, Torda AE, Gunsteren WF (1994) Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des 8:695-708. doi:10.1007/BF00124016
    • (1994) J Comput Aided Mol Des , vol.8 , pp. 695-708
    • Huber, T.1    Torda, A.E.2    Gunsteren, W.F.3
  • 52
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: conformational flooding
    • Grubmüller H (1995) Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E Stat Plasmas Fluids Retat Interdiscip Topics 52:2893-2906. doi:10.1103/PhysRevE.52.2893
    • (1995) Phys Rev E Stat Plasmas Fluids Retat Interdiscip Topics , vol.52 , pp. 2893-2906
    • Grubmller, H.1
  • 53
    • 46049120447 scopus 로고    scopus 로고
    • Stabilization of resonance states by an asymptotic Coulomb potential
    • Adamson S, Kharlampidi D, Dementiev A (2008) Stabilization of resonance states by an asymptotic Coulomb potential. J Chem Phys 128:024101. doi:10.1063/1.2821102
    • (2008) J Chem Phys , vol.128 , pp. 024101
    • Adamson, S.1    Kharlampidi, D.2    Dementiev, A.3
  • 54
    • 68949116150 scopus 로고    scopus 로고
    • Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers
    • Accessed 6 Aug 2013
    • Yesylevskyy S, Marrink S-J, Mark AE (2009) Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophys J 97: 40-49. http://www.pubmedcentral.nih. gov/articlerender.fcgi?artid=2711361&tool= pmcentrez&rendertype=abstract. Accessed 6 Aug 2013
    • (2009) Biophys J , vol.97 , pp. 40-49
    • Yesylevskyy, S.1    Marrink, S.-J.2    Mark, A.E.3
  • 55
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Yuko Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141-151
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Yuko, Y.2
  • 56
    • 0000888146 scopus 로고    scopus 로고
    • Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
    • Sugita Y, Okamoto Y (2000) Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape. Chem Phys Lett 329:261-270
    • (2000) Chem Phys Lett , vol.329 , pp. 261-270
    • Sugita, Y.1    Okamoto, Y.2
  • 57
    • 79960928036 scopus 로고    scopus 로고
    • Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2)
    • Wang L, Friesner RA, Berne BJ (2011) Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115:9431-9438. doi:10.1021/jp204407d
    • (2011) J Phys Chem B , vol.115 , pp. 9431-9438
    • Wang, L.1    Friesner, R.A.2    Berne, B.J.3
  • 58
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
    • Bussi G, Gervasio FL, Laio A, Parrinello M (2006) Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc 128:13435-13441. doi:10.1021/ja062463w
    • (2006) J Am Chem Soc , vol.128 , pp. 13435-13441
    • Bussi, G.1    Gervasio, F.L.2    Laio, A.3    Parrinello, M.4
  • 59
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: the Langevin piston method
    • Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613. doi:10.1063/1.470648
    • (1995) J Chem Phys , vol.103 , pp. 4613
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 60
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: a new molecular dynamics method
    • Parrinello M (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182. doi:10.1063/1.328693
    • (1981) J Appl Phys , vol.52 , pp. 7182
    • Parrinello, M.1
  • 61
    • 2342422492 scopus 로고    scopus 로고
    • Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions
    • Patra M, Karttunen M, Hyvönen MT, Falck E, Vattulainen I (2004) Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions. J Phys Chem B 108:4485-4494. doi:10.1021/jp031281a
    • (2004) J Phys Chem B , vol.108 , pp. 4485-4494
    • Patra, M.1    Karttunen, M.2    Hyvönen, M.T.3    Falck, E.4    Vattulainen, I.5
  • 62
    • 77950483949 scopus 로고    scopus 로고
    • Molecular simulations of antimicrobial peptides
    • Langham A, Kaznessis YN (2010) Molecular simulations of antimicrobial peptides. Methods Mol Biol 618:267-285. doi:10.1007/978-1-60761-594-1_17
    • (2010) Methods Mol Biol , vol.618 , pp. 267-285
    • Langham, A.1    Kaznessis, Y.N.2
  • 63
    • 16244363029 scopus 로고    scopus 로고
    • Simulating the self-assembly of model membranes
    • Venturoli M, Smit B (1999) Simulating the self-assembly of model membranes. Phys Chem Comm 2:45. doi:10.1039/a906472i
    • (1999) Phys Chem Comm , vol.2 , pp. 45
    • Venturoli, M.1    Smit, B.2
  • 64
    • 0036841855 scopus 로고    scopus 로고
    • Analysis and evaluation of channel models: simulations of alamethicin
    • Accessed 7 Aug 2013
    • Peter Tieleman D, Hess B, Sansom MSP (2002) Analysis and evaluation of channel models: simulations of alamethicin. Biophys J 83:2393-2407. http://linkinghub.elsevier. com/retrieve/pii/S0006349502752533. Accessed 7 Aug 2013
    • (2002) Biophys J , vol.83 , pp. 2393-2407
    • Peter Tieleman, D.1    Hess, B.2    Sansom, M.S.P.3
  • 65
    • 58149164577 scopus 로고    scopus 로고
    • Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study
    • Accessed 7 Aug 2013
    • Thøgersen L, Schiøtt B, Vosegaard T, Nielsen NC, Tajkhorshid E (2008) Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J 95:4337-4347. http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid =2567951&tool=pmcentrez&rendertype=abstr act. Accessed 7 Aug 2013
    • (2008) Biophys J , vol.95 , pp. 4337-4347
    • Thøgersen, L.1    Schiøtt, B.2    Vosegaard, T.3    Nielsen, N.C.4    Tajkhorshid, E.5
  • 66
    • 61749090359 scopus 로고    scopus 로고
    • Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer
    • Gkeka P, Sarkisov L (2009) Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer. J Phys Chem B 113:6-8. doi:10.1021/jp808417a
    • (2009) J Phys Chem B , vol.113 , pp. 6-8
    • Gkeka, P.1    Sarkisov, L.2
  • 67
    • 79959572024 scopus 로고    scopus 로고
    • Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study
    • Accessed 7 Aug 2013
    • Woo H-J, Wallqvist A (2011) Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study. J Phys Chem B 115:8122-8129. http://www.ncbi.nlm.nih. gov/pubmed/21651300. Accessed 7 Aug 2013
    • (2011) J Phys Chem B , vol.115 , pp. 8122-8129
    • Woo, H.-J.1    Wallqvist, A.2
  • 68
    • 84897694506 scopus 로고    scopus 로고
    • High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion
    • Accessed 14 Feb 2014
    • Perrin BS, Tian Y, Fu R, Grant C V, Chekmenev EY et al (2014) High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion. J Am Chem Soc. http://www.ncbi.nlm.nih.gov/pubmed/24410116. Accessed 14 Feb 2014
    • (2014) J Am Chem Soc
    • Perrin, B.S.1    Tian, Y.2    Fu, R.3    Grant, C.V.4    Chekmenev, E.Y.5
  • 69
    • 84864227931 scopus 로고    scopus 로고
    • Multiscale simulations of the antimicrobial peptide maculatin 1.1: water permeation through disordered aggregates
    • Parton DL, Akhmatskaya EV, Sansom MSP (2012) Multiscale simulations of the antimicrobial peptide maculatin 1.1: water permeation through disordered aggregates. J Phys Chem B 116:8485-8493. doi:10.1021/jp 212358y
    • (2012) J Phys Chem B , vol.116 , pp. 8485-8493
    • Parton, D.L.1    Akhmatskaya, E.V.2    Sansom, M.S.P.3


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