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Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods:  An Analysis of ALOGP and CLOGP Methods

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Department of Molecular Structure and Design, Amgen Inc., 1840 DeHavilland Drive, Thousand Oaks, California 91320
Cite this: J. Phys. Chem. A 1998, 102, 21, 3762–3772
Publication Date (Web):May 5, 1998
https://doi.org/10.1021/jp980230o
Copyright © 1998 American Chemical Society
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Abstract

Molecular hydrophobicity (lipophilicity), usually quantified as log P (the logarithm of 1-octanol/water partition coefficient), is an important molecular characteristic in drug discovery. ALOGP and CLOGP are two of the most widely used methods for the estimation of log P. This work describes an extensive reparametrization of the atomic log P values and a detailed comparison of the performance of ALOGP and CLOGP methods on the Pomona Medchem database. Only the “star list” compounds having precisely measured log P values were used in this analysis. While the overall results with both methods are similar, analysis shows that the CLOGP method is better for very small molecules in the range of 1−20 atoms. The two methods are almost comparable in the range of 21−45 atoms, while the ALOGP method has better accuracy for molecules with more than 45 atoms. Although the rms deviation and the correlation coefficient for CLOGP predictions were marginally better than those for corresponding ALOGP predictions, the latter showed a very stable performance for all classes of organic compounds analyzed. The ALOGP method can be used to compute estimates of most neutral organic compounds having C, H, O, N, S, Se, P, B, Si, and halogens. It also covers most zwitterionic compounds having amine and carboxylic acids and ammonium halide salts. The CLOGP method has improved considerably over the years to cover most neutral organic compounds, but it still has some undefined fragments. Finally, unlike CLOGP and other methods of predicting lipophilicity, the ALOGP method has multiple uses, such as the estimation of local hydrophobicity, the visualization of molecular hydrophobicity maps, and the evaluation of hydrophobic interactions in protein−ligand complexes.

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  233. Andrzej Zięba, Katarzyna Bober. Lipophilicity analysis of newly synthetized quinobenzothiazines by use of TLC. Journal of Liquid Chromatography & Related Technologies 2016, 39 (2) , 104-109. https://doi.org/10.1080/10826076.2015.1132724
  234. Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A.F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio. iPPI-DB: an online database of modulators of protein–protein interactions. Nucleic Acids Research 2016, 44 (D1) , D542-D547. https://doi.org/10.1093/nar/gkv982
  235. Matthias Nettekoven, Jean-Michel Adam, Stefanie Bendels, Catarina Bissantz, Jürgen Fingerle, Uwe Grether, Sabine Grüner, Wolfgang Guba, Atsushi Kimbara, Giorgio Ottaviani, Bernd Püllmann, Mark Rogers-Evans, Stephan Röver, Benno Rothenhäusler, Sebastien Schmitt, Franz Schuler, Tanja Schulz-Gasch, Christoph Ullmer. Novel Triazolopyrimidine-Derived Cannabinoid Receptor 2 Agonists as Potential Treatment for Inflammatory Kidney Diseases. ChemMedChem 2016, 11 (2) , 179-189. https://doi.org/10.1002/cmdc.201500218
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  239. Pravin Ambure, Kunal Roy. Understanding the structural requirements of cyclic sulfone hydroxyethylamines as hBACE1 inhibitors against Aβ plaques in Alzheimer's disease: a predictive QSAR approach. RSC Advances 2016, 6 (34) , 28171-28186. https://doi.org/10.1039/C6RA04104C
  240. Rahul Balasaheb Aher, Kunal Roy. Exploring structural requirements for the inhibition of Plasmodium falciparum calcium-dependent protein kinase-4 (PfCDPK-4) using multiple in silico approaches. RSC Advances 2016, 6 (57) , 51957-51982. https://doi.org/10.1039/C6RA05692J
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  243. Hongxin Fu, Jianying Dai, Yaqin Sun, Daijia Zhang, Zhilong Xiu. Partition behavior of hydrophilic diols in an ethanol/ammonium sulfate salting-out extraction system. Engineering in Life Sciences 2015, 15 (8) , 797-803. https://doi.org/10.1002/elsc.201400225
  244. J. L. McDonagh, T. van Mourik, J. B. O. Mitchell. Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation. Molecular Informatics 2015, 34 (11-12) , 715-724. https://doi.org/10.1002/minf.201500052
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  246. Claudia Ileana Cappelli, Emilio Benfenati, Josep Cester. Evaluation of QSAR models for predicting the partition coefficient (logP) of chemicals under the REACH regulation. Environmental Research 2015, 143 , 26-32. https://doi.org/10.1016/j.envres.2015.09.025
  247. Zhi-Hua Guo, Yong Yin, Cong Wang, Peng-Fei Wang, Xing-Tao Zhang, Zhong-Chang Wang, Hai-Liang Zhu. Design, synthesis and molecular docking of salicylic acid derivatives containing metronidazole as a new class of antimicrobial agents. Bioorganic & Medicinal Chemistry 2015, 23 (18) , 6148-6156. https://doi.org/10.1016/j.bmc.2015.07.075
  248. Yugao Guo, Shuo Ma, Shan Guan, Yan Zhang, Jie Pan. High-Throughput Determination of Octanol–Water Partition Coefficients by Ultrasound-Assisted Liquid-Phase Microextraction. Journal of Chromatographic Science 2015, 53 (8) , 1400-1406. https://doi.org/10.1093/chromsci/bmu218
  249. Gwenaëlle Sizun, Claire Pierra, Jérôme Peyronnet, Eric Badaroux, Céline Rabeson, Samira Benzaria-Prad, Dominique Surleraux, Anna Giulia Loi, Chiara Musiu, Michel Liuzzi, Maria Seifer, David Standring, Jean-Pierre Sommadossi, Gilles Gosselin. Design, synthesis and antiviral evaluation of 2′- C -methyl branched guanosine pronucleotides: the discovery of IDX184, a potent liver-targeted HCV polymerase inhibitor. Future Medicinal Chemistry 2015, 7 (13) , 1675-1700. https://doi.org/10.4155/fmc.15.96
  250. P. Fonteh, A. Elkhadir, B. Omondi, I. Guzei, J. Darkwa, D. Meyer. Impedance technology reveals correlations between cytotoxicity and lipophilicity of mono and bimetallic phosphine complexes. BioMetals 2015, 28 (4) , 653-667. https://doi.org/10.1007/s10534-015-9851-y
  251. Priya V. Parandekar, Andrea R. Browning, Om Prakash. Modeling the flammability characteristics of polymers using quantitative structure-property relationships (QSPR). Polymer Engineering & Science 2015, 55 (7) , 1553-1559. https://doi.org/10.1002/pen.24093
  252. Monique Lüthy, Mary C. Wheldon, Chehasnah Haji-Cheteh, Masakazu Atobe, Paul S. Bond, Peter O’Brien, Roderick E. Hubbard, Ian J.S. Fairlamb. Lead-oriented synthesis: Investigation of organolithium-mediated routes to 3-D scaffolds and 3-D shape analysis of a virtual lead-like library. Bioorganic & Medicinal Chemistry 2015, 23 (11) , 2680-2694. https://doi.org/10.1016/j.bmc.2015.04.005
  253. Katherine Basore, Yang Cheng, Ambuj K. Kushwaha, Son T. Nguyen, Sanjay A. Desai. How do antimalarial drugs reach their intracellular targets?. Frontiers in Pharmacology 2015, 6 https://doi.org/10.3389/fphar.2015.00091
  254. Fanny Palace-Berl, Kerly Fernanda Mesquita Pasqualoto, Salomão Dória Jorge, Bianca Zingales, Rodrigo Rocha Zorzi, Marcelo Nunes Silva, Adilson Kleber Ferreira, Ricardo Alexandre de Azevedo, Sarah Fernandes Teixeira, Leoberto Costa Tavares. Designing and exploring active N′-[(5-nitrofuran-2-yl) methylene] substituted hydrazides against three Trypanosoma cruzi strains more prevalent in Chagas disease patients. European Journal of Medicinal Chemistry 2015, 96 , 330-339. https://doi.org/10.1016/j.ejmech.2015.03.066
  255. Ignacio Aliagas, Alberto Gobbi, Timothy Heffron, Man-Ling Lee, Daniel F. Ortwine, Mark Zak, S. Cyrus Khojasteh. A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery. Journal of Computer-Aided Molecular Design 2015, 29 (4) , 327-338. https://doi.org/10.1007/s10822-015-9838-3
  256. Matthew J. Weaver, Alison K. Kearns, Sascha Stump, Chun Li, Mariusz P. Gajewski, Kevin C. Rider, Donald S. Backos, Philip R. Reigan, Howard D. Beall, Nicholas R. Natale. AIMing towards improved antitumor efficacy. Bioorganic & Medicinal Chemistry Letters 2015, 25 (8) , 1765-1770. https://doi.org/10.1016/j.bmcl.2015.02.063
  257. Supratik Kar, Kunal Roy. Predictive toxicity modelling of benzodiazepine drugs using multiple in silico approaches: descriptor-based QSTR, group-based QSTR and 3D-toxicophore mapping. Molecular Simulation 2015, 41 (4) , 345-355. https://doi.org/10.1080/08927022.2014.888718
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  259. K. Kranthi Raj, Sunny Manohar, Venkateswara Rao Talluri, Diwan S. Rawat. Insights into activity enhancement of 4-aminoquinoline-based hybrids using atom-based and field-based QSAR studies. Medicinal Chemistry Research 2015, 24 (3) , 1136-1154. https://doi.org/10.1007/s00044-014-1195-6
  260. Yong Yin, Yan-Qing Zhang, Biao Jin, Shao Sha, Xun Wu, Chetan B. Sangani, She-Feng Wang, Fang Qiao, Ai-Min Lu, Peng-Cheng Lv, Hai-Liang Zhu. 6,7-Dihydrobenzo[f]benzo[4,5]imidazo[1,2-d][1,4]oxazepine derivatives as selective inhibitors of PI3Kα. Bioorganic & Medicinal Chemistry 2015, 23 (6) , 1231-1240. https://doi.org/10.1016/j.bmc.2015.01.052
  261. Daniel Cappel, Steven L. Dixon, Woody Sherman, Jianxin Duan. Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. Journal of Computer-Aided Molecular Design 2015, 29 (2) , 165-182. https://doi.org/10.1007/s10822-014-9813-4
  262. Laszlo Tarko. QSPR for LogP using molecules without oxygen and nitrogen and quantum mechanics descriptors. Journal of the Iranian Chemical Society 2015, 12 (2) , 359-365. https://doi.org/10.1007/s13738-014-0490-y
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  268. Jonathan Villain, Sylvain Lozano, Marie-Pierre Halm-Lemeille, Gilles Durrieu, Ronan Bureau. Quantile regression model for a diverse set of chemicals: application to acute toxicity for green algae. Journal of Molecular Modeling 2014, 20 (12) https://doi.org/10.1007/s00894-014-2508-x
  269. D. M. Moss, P. Curley, A. Shone, M. Siccardi, A. Owen. A multisystem investigation of raltegravir association with intestinal tissue: implications for pre-exposure prophylaxis and eradication. Journal of Antimicrobial Chemotherapy 2014, 69 (12) , 3275-3281. https://doi.org/10.1093/jac/dku312
  270. Rodrigo S. Razo-Hernández, Kayim Pineda-Urbina, Marlene A. Velazco-Medel, Manuel Villanueva-García, M. Teresa Sumaya-Martínez, Francisco J. Martínez-Martínez, Zeferino Gómez-Sandoval. QSAR study of the DPPH· radical scavenging activity of coumarin derivatives and xanthine oxidase inhibition by molecular docking. Central European Journal of Chemistry 2014, 12 (10) , 1067-1080. https://doi.org/10.2478/s11532-014-0555-x
  271. Rahul Balasaheb Aher, Kunal Roy. QSAR and pharmacophore modeling of diverse aminothiazoles and aminopyridines for antimalarial potency against multidrug-resistant Plasmodium falciparum. Medicinal Chemistry Research 2014, 23 (9) , 4238-4249. https://doi.org/10.1007/s00044-014-0997-x
  272. Vincent Loizeau, Philippe Ciffroy, Yelva Roustan, Luc Musson-Genon. Identification of sensitive parameters in the modeling of SVOC reemission processes from soil to atmosphere. Science of The Total Environment 2014, 493 , 419-431. https://doi.org/10.1016/j.scitotenv.2014.05.136
  273. Anna Caruso, Jean-Charles Lancelot, Hussein El-Kashef, Antonella Panno, Maria Stefania Sinicropi, Rémi Legay, Aurélien Lesnard, Alban Lepailleur, Sylvain Rault. Four Partners, Three-Step, One-Pot Reaction for a Library of New 2-Alkyl(dialkyl)aminoquinazolin-4(3 H )-ones. Journal of Heterocyclic Chemistry 2014, 51 (S1) , E282-E293. https://doi.org/10.1002/jhet.1942
  274. César R. García-Jacas, Yovani Marrero-Ponce, Liesner Acevedo-Martínez, Stephen J. Barigye, José R. Valdés-Martiní, Ernesto Contreras-Torres. QuBiLS-MIDAS: A parallel free-software for molecular descriptors computation based on multilinear algebraic maps. Journal of Computational Chemistry 2014, 35 (18) , 1395-1409. https://doi.org/10.1002/jcc.23640
  275. Faisal Saeed, Ali Ahmed, Mohd Shahir Shamsir, Naomie Salim. Weighted voting-based consensus clustering for chemical structure databases. Journal of Computer-Aided Molecular Design 2014, 28 (6) , 675-684. https://doi.org/10.1007/s10822-014-9750-2
  276. Rudra Narayan Das, Kunal Roy. Predictive modeling studies for the ecotoxicity of ionic liquids towards the green algae Scenedesmus vacuolatus. Chemosphere 2014, 104 , 170-176. https://doi.org/10.1016/j.chemosphere.2013.11.002
  277. Supratik Kar, Agnieszka Gajewicz, Tomasz Puzyn, Kunal Roy. Nano-quantitative structure–activity relationship modeling using easily computable and interpretable descriptors for uptake of magnetofluorescent engineered nanoparticles in pancreatic cancer cells. Toxicology in Vitro 2014, 28 (4) , 600-606. https://doi.org/10.1016/j.tiv.2013.12.018
  278. Sulong Xiao, Qi Wang, Longlong Si, Yongying Shi, Han Wang, Fei Yu, Yongmin Zhang, Yingbo Li, Yongxiang Zheng, Chuanling Zhang, Chunguang Wang, Lihe Zhang, Demin Zhou. Synthesis and Anti-HCV Entry Activity Studies of β-Cyclodextrin-Pentacyclic Triterpene Conjugates. ChemMedChem 2014, 9 (5) , 1060-1070. https://doi.org/10.1002/cmdc.201300545
  279. Rodrigo Rocha Zorzi, Salomão Dória Jorge, Fanny Palace-Berl, Kerly Fernanda Mesquita Pasqualoto, Leandro de Sá Bortolozzo, André Murillo de Castro Siqueira, Leoberto Costa Tavares. Exploring 5-nitrofuran derivatives against nosocomial pathogens: Synthesis, antimicrobial activity and chemometric analysis. Bioorganic & Medicinal Chemistry 2014, 22 (10) , 2844-2854. https://doi.org/10.1016/j.bmc.2014.03.044
  280. A. S. Kuznetsov, P. V. Dubovskii, O. V. Vorontsova, A. V. Feofanov, R. G. Efremov. Interaction of linear cationic peptides with phospholipid membranes and polymers of sialic acid. Biochemistry (Moscow) 2014, 79 (5) , 459-468. https://doi.org/10.1134/S0006297914050101
  281. F. Grisoni, M. Cassotti, R. Todeschini. Reshaped Sequential Replacement for variable selection in QSPR: comparison with other reference methods. Journal of Chemometrics 2014, 28 (4) , 249-259. https://doi.org/10.1002/cem.2603
  282. Nan An, Farid Van Der Mei, Adelina Voutchkova-Kostal. Global Model for Octanol-Water Partition Coefficients from Proton Nuclear Magnetic Resonance Spectra. Molecular Informatics 2014, 33 (4) , 286-292. https://doi.org/10.1002/minf.201300172
  283. Zbigniew J. Witczak, Tomasz Poplawski, Anna Czubatka, Joanna Sarnik, Pawel Tokarz, Adam L. VanWert, Roman Bielski. A potential CARB-pharmacophore for antineoplastic activity: Part 1. Bioorganic & Medicinal Chemistry Letters 2014, 24 (7) , 1752-1757. https://doi.org/10.1016/j.bmcl.2014.02.036
  284. Stefan Dove, Kerstin Yvonne Danker, Johannes-Peter Stasch, Volkhard Kaever, Roland Seifert. Structure/Activity Relationships of (M)ANT- and TNP-Nucleotides for Inhibition of Rat Soluble Guanylyl Cyclase α1β1. Molecular Pharmacology 2014, 85 (4) , 598-607. https://doi.org/10.1124/mol.113.091017
  285. Fabio Dall’Antonia, Tea Pavkov-Keller, Klaus Zangger, Walter Keller. Structure of allergens and structure based epitope predictions. Methods 2014, 66 (1) , 3-21. https://doi.org/10.1016/j.ymeth.2013.07.024
  286. Mihai V. Putz, Nicoleta A. Dudaş. Variational principles for mechanistic quantitative structure–activity relationship (QSAR) studies: application on uracil derivatives’ anti-HIV action. Structural Chemistry 2013, 24 (6) , 1873-1893. https://doi.org/10.1007/s11224-013-0249-6
  287. Lei Yuwen, Feng-Li Zhang, Qi-Hua Chen, Shuang-Jun Lin, Yi-Lei Zhao, Zhi-Yong Li. The role of aromatic L-amino acid decarboxylase in bacillamide C biosynthesis by Bacillus atrophaeus C89. Scientific Reports 2013, 3 (1) https://doi.org/10.1038/srep01753
  288. A. Nandy, S. Kar, K. Roy. Development and validation of regression-based QSAR models for quantification of contributions of molecular fragments to skin sensitization potency of diverse organic chemicals. SAR and QSAR in Environmental Research 2013, 24 (12) , 1009-1023. https://doi.org/10.1080/1062936X.2013.821422
  289. Vipul M. Buha, Dharmaraj N. Rana, Mahesh T. Chhabria, Kishor H. Chikhalia, Bhushan M. Mahajan, Pathik S. Brahmkshatriya, Nisha K. Shah. Synthesis, biological evaluation and QSAR study of a series of substituted quinazolines as antimicrobial agents. Medicinal Chemistry Research 2013, 22 (9) , 4096-4109. https://doi.org/10.1007/s00044-012-0408-0
  290. Fanny Palace-Berl, Salomão Dória Jorge, Kerly Fernanda Mesquita Pasqualoto, Adilson Kleber Ferreira, Durvanei Augusto Maria, Rodrigo Rocha Zorzi, Leandro de Sá Bortolozzo, José Ângelo Lauletta Lindoso, Leoberto Costa Tavares. 5-Nitro-2-furfuriliden derivatives as potential anti-Trypanosoma cruzi agents: Design, synthesis, bioactivity evaluation, cytotoxicity and exploratory data analysis. Bioorganic & Medicinal Chemistry 2013, 21 (17) , 5395-5406. https://doi.org/10.1016/j.bmc.2013.06.017
  291. Dhanaji S. Gond, Rohan J. Meshram, Sharad G. Jadhav, Gulshan Wadhwa, Rajesh N. Gacche. In silico screening of chalcone derivatives as potential inhibitors of dihydrofolate reductase: Assessment using molecular docking, paired potential and molecular hydrophobic potential studies. Drug Invention Today 2013, 5 (3) , 182-191. https://doi.org/10.1016/j.dit.2013.08.003
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  293. Holger Kubas, Udo Meyer, Bjoern Krueger, Mirko Hechenberger, Maksims Vanejevs, Ronalds Zemribo, Valerjans Kauss, Raisa Ambartsumova, Ilya Pyatkin, Alexey I. Polosukhin, Ulrich Abel. Discovery, synthesis, and structure–activity relationships of 2-aminoquinazoline derivatives as a novel class of metabotropic glutamate receptor 5 negative allosteric modulators. Bioorganic & Medicinal Chemistry Letters 2013, 23 (16) , 4493-4500. https://doi.org/10.1016/j.bmcl.2013.06.049
  294. George Papadatos, Nathan Brown. In silico applications of bioisosterism in contemporary medicinal chemistry practice. Wiley Interdisciplinary Reviews: Computational Molecular Science 2013, 3 (4) , 339-354. https://doi.org/10.1002/wcms.1148
  295. Anton O. Chugunov, Anna D. Koromyslova, Antonina A. Berkut, Steve Peigneur, Jan Tytgat, Anton A. Polyansky, Vladimir M. Pentkovsky, Alexander A. Vassilevski, Eugene V. Grishin, Roman G. Efremov. Modular Organization of α-Toxins from Scorpion Venom Mirrors Domain Structure of Their Targets, Sodium Channels. Journal of Biological Chemistry 2013, 288 (26) , 19014-19027. https://doi.org/10.1074/jbc.M112.431650
  296. Iwona E. Weidlich, Igor V. Filippov, Jodian Brown, Neerja Kaushik-Basu, Ramalingam Krishnan, Marc C. Nicklaus, Ian F. Thorpe. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorganic & Medicinal Chemistry 2013, 21 (11) , 3127-3137. https://doi.org/10.1016/j.bmc.2013.03.032
  297. Lee D. Fader, Serge Landry, Sylvie Goulet, Sébastien Morin, Stephen H. Kawai, Yves Bousquet, Isabelle Dion, Oliver Hucke, Nathalie Goudreau, Christopher T. Lemke, Jean Rancourt, Pierre Bonneau, Steve Titolo, Ma’an Amad, Michel Garneau, Jianmin Duan, Stephen Mason, Bruno Simoneau. Optimization of a 1,5-dihydrobenzo[b][1,4]diazepine-2,4-dione series of HIV capsid assembly inhibitors 2: Structure–activity relationships (SAR) of the C3-phenyl moiety. Bioorganic & Medicinal Chemistry Letters 2013, 23 (11) , 3401-3405. https://doi.org/10.1016/j.bmcl.2013.03.074
  298. Kunal Roy, Rudra Narayan Das. QSTR with extended topochemical atom (ETA) indices. 16. Development of predictive classification and regression models for toxicity of ionic liquids towards Daphnia magna. Journal of Hazardous Materials 2013, 254-255 , 166-178. https://doi.org/10.1016/j.jhazmat.2013.03.023
  299. Ramanuj P. Samal, Vijay M. Khedkar, Raghuvir R. S. Pissurlenkar, Angela Gono Bwalya, Deniz Tasdemir, Ramesh A. Joshi, P. R. Rajamohanan, Vedavati G. Puranik, Evans C. Coutinho. Design, Synthesis, Structural Characterization by IR, 1 H, 13 C, 15 N, 2D-NMR, X-Ray Diffraction and Evaluation of a New Class of Phenylaminoacetic Acid Benzylidene Hydrazines as pf ENR Inhibitors. Chemical Biology & Drug Design 2013, 81 (6) , 715-729. https://doi.org/10.1111/cbdd.12118
  300. Nabanita Saikia, Sanchaita Rajkhowa, Ramesh C. Deka. Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein. Journal of Computer-Aided Molecular Design 2013, 27 (3) , 257-276. https://doi.org/10.1007/s10822-013-9638-6
  301. Faisal Saeed, Naomie Salim, Ammar Abdo, Hamza Hentabli. Graph-Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures. Molecular Informatics 2013, 32 (2) , 165-178. https://doi.org/10.1002/minf.201200110
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