1 1. Meet Our Editor. Dr. Subhash C. Basak. Natural Resources Research Institute and Department of Chemistry & Biochemistry. University of Minnesota Duluth.
Meet Our Editor
Current Computer-Aided Drug Design, 2017, Vol. 13, No. 1
1
Meet Our Editor Dr. Subhash C. Basak Natural Resources Research Institute and Department of Chemistry & Biochemistry University of Minnesota Duluth USA Dr. Subhash C. Basak is a Senior Scientist at the Natural Resources Research Institute and an Adjunct Professor at the Department of Chemistry and Biochemistry, University of Minnesota Duluth, USA. Dr. Basak received his PhD degree in biochemistry from the University of Calcutta. During the past four decades he has pioneered research in the development of novel mathematical chemodescriptors and biodescriptors principally via applications of discrete mathematics on chemical and biological systems. He also published extensively on the use of such descriptors along with proper statistical methods in drug design, predictive toxicology, characterization of emerging pathogens as well as nanotoxicology. Some specific areas of his research include: a) Formulation of new topological indices, b) Study of intercorrelation of molecular descriptors, c) Hierarchical quantitative structure-activity relationship (HiQSAR) studies using topological, geometrical, and quantum chemical descriptors, d) Formulation of quantitative molecular similarity analysis (QMSA) and tailored QMSA methods for analog selection, e) Use of QMSA methods in the analysis of large combinatorial libraries, f) Development of new descriptors for the characterization of DNA/ RNA sequences, g) Exploration of novel mathematical techniques for the quantification of the proteomics maps, h) Development of new indices for the characterization of molecular chirality, i) Differential QSAR (DiffQSAR) model formulation to understand molecular basis of drug resistance, j) Use of algorithmically calculated descriptors to predict toxic modes of action of pollutants, k) Use of computational chemistry in the design of novel mosquito repellents, l) Mathematical nanotoxicoproteomics, m) Study of proper statistical methods for assessing model fit by cross-validation, n) Explore Intrinsic Dimensionality of Chemical Spaces for Robust QSAR Model Development, o) Study the role of Big Data in New Drug Discovery, p) Computer-Assisted Approaches to Rational Design of Peptide Vaccines, and q) Explore the philosophical basis of mathematical chemistry. He has collaborated with over fifty research scientists located in four continents, viz., Asia, Europe, North America, and South America, whom he fondly calls members of his “virtual team”. Such collaborations (Fig. 1) resulted in the publication of more than 230 peer reviewed journal articles, book chapters, and reviews. Dr. Basak and coworkers developed three software, viz. POLLY, APProbe, and Triplet, for the calculation of molecular chemodescriptors of chemicals. Such software found applications in pharmaceutical drug design by companies, quantitative structure-activity/ property relationship (QSAR/ QSPR) studies for property/ bioactivity estimation, and hazard assessment of chemicals. He edited two books, one on network analysis published by Wiley and the other is a two volume comprehensive treatise on mathematical chemistry and its applications published by Bentham Science Publishers and Elsevier. Dr. Basak has been Chairperson from USA of two continuing international workshop series on mathematical chemistry and since 1998 organized thirteen international workshops on mathematical chemistry in North America, South America, and Asia. During the past three decades Dr. Basak received more than 6 million US dollars in research grants and contracts from various private and public funding agencies.
Geographical distribution of Subhash Basak’s global research collaboration and Technology gy Transfer Canada Design of Mineral Floatation Agents
Italy
Slovenia
Predict Toxicity of Environmental Pollutants
Develop Bioinformatics Tools
USA
China
Design HIV Drugs
Quantify DNA Sequences
Colombia India Design of Malaria and Leishmaniasis Drugs g (Tropical Diseases)
• Design TB Drugs • Design Malaria Drugs • Characterize Bird Flu
Thailand Design Mosquito Repellents
Fig. (1). Geographical distribution of Subhash Basak’s global research collaboration and Technology Transfer. 1875-6697/17 $58.00+.00
© 2017 Bentham Science Publishers
2 Current Computer-Aided Drug Design, 2017, Vol. 13, No. 1
Meet Our Editor
SELECTED PUBLICATIONS [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34]
Basak, S.C.; Restrepo, G.; Villaveces, J.L.; Eds. Advances in Mathematical Chemistry and Applications. Elsevier: Amsterdam 2016, Vol. 1-2. Dehmer, M.; Basak S.C.; Eds. Statistical and Machine Learning Approaches for Network Analysis. Wiley & Sons: New Jersey, USA, 2012. Basak, S.C.; Magnuson, V.R. Molecular topology and narcosis: A quantitative structure-activity relationship (QSAR) study of alcohols using complementary information content (CIC). Arzneim- Forsch/Drug Res., 1983, 33, 501-503. Raychaudhury, C.; Ray, S.K.; Ghosh, J.J.; Roy, A.B.; Basak, S.C. Discrimination of isomeric structures using information-theoretic topological indices. J. Comput. Chem., 1984, 5, 581-588. Balaban, A.T.; Mills, D.; Ivanciuc, O.; Basak, S.C. Reverse Wiener indices. Croat. Chem. Acta, 2000, 73, 923-941. Trinajstic, N.; Nikolic, S.; Basak, S.C.; Lukovits, I. Distance indices and their hyper-counterparts: Intercorrelation and use in the structure-property modeling. SAR QSAR Environ. Res., 2001, 12, 31-54. Basak, S.C.; Magnuson, V.R.; Niemi, G.J.; Regal, R.R.; Veith, G.D. Topological indices: their nature, mutual relatedness, and applications. Math. Model., 1987, 8, 300-305. Basak, S.C., Gute, B.D.; Grunwald, G.D. Use of topostructural, topochemical, and geometric parameters in the prediction of vapor pressure: A hierarchical approach. J. Chem. Inf. Comput. Sci., 1997, 37, 651-655 Balasubramanian, K.; Basak, S.C. Characterization of isospectral graphs using graph invariants and derived orthogonal parameters. J. Chem. Inf. Comput. Sci., 1998, 38, 367-373. Basak, S.C.; Magnuson, V.R.; Niemi, G.J.; Regal, R.R. Determining structural similarity of chemicals using graph theoretic indices. Discrete Appl. Math., 1988, 19, 17-44. Basak, S.C.; Niemi, G.J.; Veith, G.D. Optimal characterization of structure for prediction of properties. J. Math. Chem., 1990, 4, 185205. Basak, S.C.; Gute, B.D.; Mills, D.; Hawkins, D.M. Quantitative molecular similarity methods in the property/toxicity estimation of chemicals: A comparison of arbitrary versus tailored similarity spaces. J. Mol. Struct. Theochem., 2003, 622, 127-145 Basak, S.C.; Grunwald, G.D. Tolerance space and molecular similarity. SAR QSAR Environ. Res., 1995, 3, 265-277. Basak, S.C.; Mills, D.; Gute, B.; Balaban, A.T.; Basak, K.; Grunwald, G.D. Use of mathematical structural invariants in analyzing combinatorial libraries: a case study with psoralen derivatives. Curr. Comput. Aided Drug Des., 2010, 6, 240-251. Nandy, A.; Harle, M.; Basak, S.C. Mathematical descriptors of DNA sequences: development and applications. Arkivoc, 2006, 9, 211238. Guo, X.; Randic, M.; Basak, S.C. A novel 2-D graphical representation of DNA sequences of low degeneracy. Chem. Phys. Lett., 2001, 350, 106-112. Randic, M.; Vracko, M.; Nandy, A.; Basak, S.C. On 3-D representation of DNA primary sequences. J. Chem. Inf. Comput. Sci., 2000, 40, 1235-1244. Randic, M.; Witzmann, F.; Vracko, M.; Basak, S.C. On characterization of proteomics maps and chemically induced changes in proteomes using matrix invariants: application to peroxisome proliferators. Med. Chem. Res., 2001, 10, 456-479. Basak, S.C. Role of mathematical chemodescriptors and proteomics-based biodescriptors in drug discovery. Drug Dev. Res., 2010, 72, 1-9. Basak, S.C.; Gute, B.D. Mathematical descriptors of proteomics maps: Background and applications. Curr. Opin. Drug Discov. Devel., 2008, 11, 320-326. Vracko, M.; Basak, S.C. Similarity study of proteomic maps. Chemometr. Intell. Lab. Syst., 2004, 70, 33-38. Randic, M.; Vracko, M.; Novic, M.; Basak, S.C. On ordering of folded structures, mathematical chemistry. MATCH, 2000, 42, 181231. Bielinska-Waz, D.; Waz, P.; Basak, S.C. Statistical theory of spectra: Statistical moments as descriptors in the theory of molecular similarity. Eur. Phys. J. B., 2006, 50, 333-338. Natarajan, R.; Basak, S.C.; Neumann, T. A novel approach for the numerical characterization of molecular chirality. J. Chem. Inf. Comput. Sci., 2007, 47, 771-775. Basak, S.C.; Mills, D.; Hawkins, D.M. Characterization of dihydrofolate reductases from multiple strains of Plasmodium falciparum using mathematical descriptors of their inhibitors. Chem. Biodivers., 2011, 8, 440-453. Basak, S.C.; Grunwald, G.D.; Host, G.E.; Niemi, G.J.; Bradbury, S.P. A comparative study of molecular similarity, statistical and neural network methods for predicting toxic modes of action of chemicals. Environ. Toxicol. Chem., 1998, 17, 1056-1064. Miszta, P.; Basak, S.C.; Natarajan, R.; Nowak, W. How computational studies of mosquito repellents contribute to the control of vector borne diseases. Curr. Comput. Aided Drug Des., 2013, 9, 300-307. Natarajan, R.; Basak, S.C.; Balaban A.T.; Klun J.A.; Schmidt, W.F. Chirality index, molecular overlay and biological activity of diastereoisomeric mosquito repellents. Pest. Manag. Sci., 2005, 61, 1193-1201. Basak, S.C.; Vracko, M.; Witzmann, F. Mathematical nanotoxicoproteomics: Quantitative characterization of effects of multi-walled carbon nanotubes (MWCNT) and TiO2 nanobelts (TiO2-NB) on protein expression patterns in human intestinal cells. Curr. Comput. Aided Drug Des., 2016, 12, 259-264. Basak, S.C.; Gute, B.D.; Drewes, L.R. Predicting blood-brain transport of drugs: A computational approach. Pharm. Res., 1996, 13, 775-778. Basak, S.C.; Mills, D.; El-Masri, H.A.; Mumtaz, M.M.; Hawkins, D.M. Predicting blood: air partition coefficients using theoretical molecular descriptors. Environ. Toxicol. Pharmacol., 2004, 16, 45-55. Balaban, A.T.; Basak, S.C.; Colburn, T.; Grunwald, G.D. Correlation between structure and normal boiling points of haloalkanes C1C4 using neural networks. J. Chem. Inf. Comput. Sci., 1994, 34, 1118-1121. Banerjee, B.; Basak, S.C.; Ghosh, J.J. Plasma target enzyme desensitization following chronic morphine treatment in rats. IRCS Med. Sci.,1981, 9, 929-630. Majumdar, S.; Basak, S.C. Exploring intrinsic dimensionality of chemical spaces for robust QSAR model Development: A comparison of several statistical approaches. Curr. Comput. Aided Drug Des., 2016, 12, 294-301.
Meet Our Editor
[35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Current Computer-Aided Drug Design, 2017, Vol. 13, No. 1
3
Hawkins, D.M.; Basak, S.C.; Mills, D. Assessing model fit by cross-validation. J. Chem. Inf. Comput. Sci., 2003, 43, 579-586. Hawkins, D.M.; Basak, S.C; Shi. X. QSAR with few compounds and many features. J. Chem. Inf. Comput. Sci., 2001, 41, 663-670. Basak, S.C. Mathematical descriptors for the prediction of property, bioactivity, and toxicity of chemicals from their Structure: A Chemical-Cum-Biochemical approach. Curr. Comput. Aided Drug Des., 2013, 9, 449-462. Kraker, J.J.; Hawkins, D.M.; Basak, S.C.; Natarajan, R.; Mills, D. Quantitative structure-activity relationship (QSAR) modeling of juvenile hormone activity: Comparison of validation procedures. Chemometr. Intell. Lab. Syst., 2007, 87, 33-42. Balaban, A.T.; Mills, D.; Kodali, V.; Basak, S.C. Complexity of chemical graphs in terms of size, branching, and cyclicity. SAR QSAR Environ. Res., 2006, 17, 429-450. MolconnZ. Version 4.05, Hall Ass. Consult. Quincy, MA, 2003. Basak, S.C.; Harriss, D.K.; Magnuson, V.R. POLLY v. 2.3. Copyright of the University of Minnesota, USA, 1988. Basak, S.C.; Grunwald, G.D. APProbe. Copyright of the University of Minnesota, USA, 1993. Basak, S.C.; Grunwald, G.; Balaban, A. TRIPLET; Copyright of the University of Minnesota, 1993. Basak, S.C.; Bhattacharjee, A.K. Importance of experimental validation of pharmacophore based virtual screening of compound databases. Curr. Comput. Aided Drug Des., 2015, 11(2), 1-3. Randic, M.; Basak, S.C. On use of the variable connectivity index 1f in QSAR: Toxicity of aliphatic ethers. J. Chem. Inf. Comput. Sci., 2001, 41, 614-618. Majumdar, S.; Basak, S.C.; Grunwald, G.D. Adapting interrelated two-way clustering method for quantitative structure-activity relationship (QSAR) modeling of mutagenicity/non-mutagenicity of a diverse set of chemicals. Curr. Comput. Aided Drug Des., 2013, 9, 463-471. Basak, S.C., Philosophy of mathematical Chemistry: A personal perspective. HYLE—Int. J. Philos. Chem., 2013, 19, 3-17. Basak, S.C., Vracko, M.; Bhattacharjee, A.K. Big data and new drug Discovery: Tackling “Big Data” for virtual screening of large compound databases. Curr. Comput. Aided Drug Des., 2015, 11, 197-201. Nandy, A.; Basak, S.C. A brief review of Computer-Assisted approaches to rational design of peptide vaccines. Int. J. Mol. Sci., 2016, 17, 666; doi:10.3390/ijms17050666. Basak, S.C.; Majumdar, S. Exploring two QSAR Paradigms-Congenericity principle versus diversity begets diversity principle analyzed using computed mathematical chemodescriptors of homogeneous and diverse sets of chemical mutagens. Curr. Comput. Aided Drug Des., 2016, 12, 1-3. Hawkins, D.M.; Basak, S.C.; Kraker, J.J.; Geiss, K.T.; Witzmann, F.A. Combining chemodescriptors and biodescriptors in quantitative structure - activity relationship modeling. J. Chem. Inf. Comput. Sci., 2006, 46, 9-16. Bhattacharjee, A.K.; Basak, S.C. Spilled over emerging infectious diseases necessitate an accelerated drug design and discovery Program: Some comments with special reference to chemoinformatics and the current Zika virus crisis. Curr. Comput. Aided Drug Des., 2016, 12, 251-252. Basak, S.C.; Zhu, Q.; Mills, D. Quantitative structure-activity relationships for anticancer activity of 2-phenylindoles using mathematical molecular descriptors. Curr. Comput. Aided Drug Des., 2011, 7, 98-108.
