ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation
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Todeschini R, Consonni V (2008) Handbook of molecular descriptors, vol 11. Wiley, New Jersey
Geppert H, Vogt M, Bajorath J (2010) Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation. J Chem Inf Model 50(2):205–216
Roy K, Mitra I (2012) Electrotopological state atom (E-state) index in drug design, QSAR, property prediction and toxicity assessment. Curr Comput Aided Drug Des 8(2):135–158
Berenger F, Voet A, Lee XY, Zhang KYJ (2014) A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. J Cheminformatics 6:23
Viswanadhan VN, Rajesh H, Balaji VN (2011) Atom type preferences, structural diversity, and property profiles of known drugs, leads, and nondrugs: a comparative assessment. Acs Comb Sci 13(3):327–336
Cao D, Zhou G, Liu S, Zhang L, Xu Q, He M, Liang Y (2013) Large-scale prediction of human kinase-inhibitor interactions using protein sequences and molecular topological structures. Anal Chim Acta 792:10–18
Khan MTH (2010) Predictions of the ADMET properties of candidate drug molecules utilizing different QSAR/QSPR modelling approaches. Curr Drug Metab 11(4):285–295
Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y (2012) admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model 52(11):3099–3105
Willett P (2006) Similarity-based virtual screening using 2D fingerprints. Drug Discov Today 11(23–24):1046–1053
Cereto-Massague A, Jose Ojeda M, Valls C, Mulero M, Garcia-Vallve S, Pujadas G (2015) Molecular fingerprint similarity search in virtual screening. Methods 71:58–63
Heikamp K, Bajorath J (2012) Fingerprint design and engineering strategies: rationalizing and improving similarity search performance. Future Med Chem 4(15SI):1945–1959
Cao D, Dong J, Wang N, Wen M, Deng B, Zeng W, Xu Q, Liang Y, Lu A, Chen AF (2015) In silico toxicity prediction of chemicals from EPA toxicity database by kernel fusion-based support vector machines. Chemometr Intell Lab 146:494–502
Cao D, Yang Y, Zhao J, Yan J, Liu S, Hu Q, Xu Q, Liang Y (2012) Computer-aided prediction of toxicity with substructure pattern and random forest. J Chemometr 26(1):7–15
Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V (2010) Advances in computational methods to predict the biological activity of compounds. Expert Opin Drug Dis 5(7):633–654
Lv W, Xue Y (2010) Prediction of acetylcholinesterase inhibitors and characterization of correlative molecular descriptors by machine learning methods. Eur J Med Chem 45(3):1167–1172
Kombo DC, Tallapragada K, Jain R, Chewning J, Mazurov AA, Speake JD, Hauser TA, Toler S (2013) 3D molecular descriptors important for clinical success. J Chem Inf Model 53(2):327–342
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P (2008) Drug target identification using side-effect similarity. Science 321(5886):263–266
Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK (2007) Relating protein pharmacology by ligand chemistry. Nat Biotechnol 25(2):197–206
He Z, Zhang J, Shi X, Hu L, Kong X, Cai Y, Chou K (2010) Predicting drug-target interaction networks based on functional groups and biological features. Plos One 5(3):e9603
van Westen GJP, Wegner JK, IJzerman AP, van Vlijmen HWT, Bender A (2011) Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets. Medchemcomm 2(1):16–30
Strombergsson H, Lapins M, Kleywegt GJ, Wikberg JLES (2010) Towards proteome-wide interaction models using the proteochemometrics approach. Mol Inform 29(6–7):499–508
Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, Byers SW (2012) Predicting new indications for approved drugs using a proteochemometric method. J Med Chem 55(15):6832–6848
Perot S, Sperandio O, Miteva MA, Camproux A, Villoutreix BO (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov Today 15(15–16):656–667
Cao D, Xiao N, Xu Q, Chen AF (2015) Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. Bioinformatics 31(2):279–281
Gonzalez-Diaz H, Vilar S, Santana L, Uriarte E (2007) Medicinal chemistry and bioinformatics-current trends in drugs discovery with networks topological indices. Curr Top Med Chem 7(10):1015–1029
Dimitrov I, Naneva L, Doytchinova I, Bangov I (2014) AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics 30(6):846–851
DRAGON ( http://www.talete.mi.it/products/dragon_description.htm ). Accessed 1 Dec 2015
BlueDesc ( http://www.ra.cs.uni-tuebingen.de/software/bluedesc/welcome_e.html ). Accessed 1 Dec 2015
CDK Descriptor Calculator ( http://www.rguha.net/code/java/cdkdesc.html ). Accessed 1 Dec 2015
Yap CW (2011) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32(7):1466–1474
Mold2 ( http://www.fda.gov/ScienceResearch/BioinformaticsTools/Mold2/default.htm ). Accessed 1 Dec 2015
ChemAxon JChem ( https://www.chemaxon.com/ ). Accessed 1 Dec 2015
ADMEWORKS ModelBuilder ( http://www.fqs.pl/chemistry_materials_life_science/products/ )
CDK [ http://sourceforge.net/projects/cdk ]
RDKit ( http://sourceforge.net/projects/rdkit/ )
Cao D, Xu Q, Hu Q, Liang Y (2013) ChemoPy: freely available python package for computational biology and chemoinformatics. Bioinformatics 29(8):1092–1094
MOE ( http://www.chemcomp.com/ )
SYBYL-X [ http://www.certara.com/products/molmod/sybyl-x ]
Discovery Studio ( http://accelrys.com/products/discovery-studio/ )
Mopac ( http://openmopac.net/ )
Stewart JJP (2013) Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J Mol Model 19(1):1–32
Stewart JJP (2012) Mopac 2012. Colorado Springs, CO
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open babel: An open chemical toolbox. J Cheminformatics 3:33
Hinselmann G, Rosenbaum L, Jahn A, Fechner N, Zell A (2011) jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints. J Cheminformatics 3:3
JSDraw ( http://www.scilligence.com/web/jsdraw.aspx ). Accessed 1 Dec 2015
Venn Diagram ( https://github.com/benfred/venn.js )
Cao D, Liang Y, Yan J, Tan G, Xu Q, Liu S (2013) PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies. J Chem Inf Model 53(11):3086–3096
Cortes-Ciriano I, van Westen GJP, Lenselink EB, Murrell DS, Bender A, Malliavin T (2014) Proteochemometric modeling in a Bayesian framework. J Cheminformatics 6:35