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Chakraborti, Asit K., Gopalakrishnan, B., Sobhia, M. Elizabeth and Malde, Alpeshkumar (2003) 3D-QSAR studies of indole derivatives as phosphodiesterase IV inhibitors. European Journal of Medicinal Chemistry, 38 11-12: 975-982. doi:10.1016/j.ejmech.2003.09.001 78   20 Cited 25 times in Scopus25 0
Chakraborti, A. K., Gopalakrishnan, B., Sobhi, M. E. and Malde, A. K. (2003) 3D-QSAR Studies on Thieno[3,2-d]pyrimidines as Phosphodiesterase IV Inhibitors. Bioorganic & Medicinal Chemistry Letters, 13 8: 1403-1408. doi:10.1016/S0960-894X(03)00172-0 126   24 Cited 29 times in Scopus29 0
Nayyar, Amit, Malde, Alpeshkumar, Jain, Rahul and Coutinho, E. (2006) 3D-QSAR study of ring-substituted quinoline class of anti-tuberculosis agents. Bioorganic & Medicinal Chemistry, 14 3: 847-856. doi:10.1016/j.bmc.2005.09.018 178   60 Cited 62 times in Scopus62 0
Verma, Jitender, Khedkar, Vijay M., Prabhu, Arati S., Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2008) A comprehensive analysis of the thermodynamic events involved in ligand–receptor binding using CoRIA and its variants. Journal of Computer-Aided Molecular Design, 22 2: 91-104. doi:10.1007/s10822-008-9172-0 68   12 Cited 15 times in Scopus15 0
Saez, Natalie J., Mobli, Mehdi, Bieri, Michael, Chassagnon, Irene R., Malde, Alpeshkumar K., Gamsjaeger, Roland, Mark, Alan E., Gooley, Paul R., Rash. Lachlan D. and King, Glenn F. (2011) A dynamic pharmacophore drives the interaction between psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a. Molecular Pharmacology, 80 5: 796-808. doi:10.1124/mol.111.072207 141   23 Cited 23 times in Scopus23 0
Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris and Mark, Alan E. (2011) An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7 12: 4026-4037. doi:10.1021/ct200196m 151   99 Cited 103 times in Scopus103 2
Malde, Alpeshkumar K. and Mark, Alan E. (2009) Binding and enantiomeric selectivity of threonyl-tRNA synthetase. Journal of the American Chemical Society, 131 11: 3848-3849. doi:10.1021/ja9002124 87   7 Cited 7 times in Scopus7 0
Malde, AK and Mark, AE (2011) Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. Journal of Computer-Aided Molecular Design, 25 1: 1-12. doi:10.1007/s10822-010-9397-6 103   16 Cited 15 times in Scopus15 8
Canzar, Stefan, El-Kebir, Mohammed, Pool, Rene, Elbassioni, Khaled, Malde, Alpesh K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2012). Charge group partitioning in biomolecular simulation. In: Benny Chor, Proceedings: 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012. 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, (29-43). 21 - 24 April 2012. doi:10.1007/978-3-642-29627-7_3 114   Cited 1 times in Scopus1 1
Canzar, Stefan, El-Kebir, Mohammed, Pool, René, Elbassioni, Khaled, Malde, Alpeshkumar K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2013) Charge group partitioning in biomolecular simulation. Journal of Computational Biology, 20 3: 188-198. doi:10.1089/cmb.2012.0239 94   7 Cited 7 times in Scopus7 2
Malde, A. K. and Galande, A. (1999) Combinatorial Libraries of Peptides, Peptoids and Cyclic Peptides. Indian Drugs, 36 10: 619-627. 27  
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2007) CoMFA study of distamycin analogs binding to the minor-groove of DNA: a unified model for broad-spectrum activity. Journal of Molecular Modeling, 13 10: 1099-1108. doi:10.1007/s00894-007-0234-3 35   5 Cited 5 times in Scopus5 0
Chakraborti, A. K., Gopalakrishnan, B., Sobhi, M. E. and Malde A.K. (2003) Comparative Molecular Field Analysis (CoMFA) of Phthalazine Derivatives as Phosphodiesterase IV Inhibitors. Bioorganic & Medicinal Chemistry Letters, 13 15: 2473-2479. doi:10.1016/S0960-894X(03)00493-1 40   21 Cited 25 times in Scopus25 0
Verma, Jitender, Malde, Alpeshkumar, Khedkar, Santosh and Coutinho, Evans (2012) Comparative occupancy analysis (CoOAn)- a straightforward and directly applicable 3D-QSAR formalism to extract molecular features obligatory for designing potent leads. Molecular Informatics, 31 6-7: 431-442. doi:10.1002/minf.201100134 27   0 Cited 0 times in Scopus0 0
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2005) Comparative protein modeling of methionine S-adenosyltransferase (MAT) enzyme from Mycobacterium tuberculosis: A potential target for antituberculosis drug discovery. Journal of Molecular Graphics and Modelling, 23 4: 355-366. doi:10.1016/j.jmgm.2004.11.003 71   6 Cited 7 times in Scopus7 0
Datar, Prasanna A., Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2006) Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands. Journal of Computer-Aided Molecular Design, 20 6: 343-360. doi:10.1007/s10822-006-9051-5 90   19 Cited 21 times in Scopus21 0
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2007) Design of Inhibitors of the MurF Enzyme of Streptococcus pneumoniae Using Docking, 3D-QSAR, and de Novo Design. Journal of Chemical Information & Modeling, 47 5: 1839-1846. doi:10.1021/ci600568u 62   16 Cited 18 times in Scopus18 0
Song, Benben, Kibler, Patrick, Malde, Alpeshkumar, Kodukula, Krishna and Galande, Amit K. (2010) Design of short linear peptides that show hydrogen bonding constraints in water. Journal of the Americal Chemical Society, 132 13: 4508-4509. doi:10.1021/ja905341p 50   12 Cited 12 times in Scopus12 0
Bharatam, P. V., Iqbal, P., Malde, A. and Tiwari, R. (2004) Electron Delocalization in Aminoguanidine: A Computational Study. The Journal of Physical Chemistry A, 108 47: 10509-10517. doi:10.1021/jp049366e 78   36 Cited 33 times in Scopus33 0
Pissurlenkar, Raghuvir R. S., Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho , Evans C. (2007) Encoding Type and Position in Peptide QSAR: Application to Peptides Binding to Class I MHC Molecule HLA-A*0201. QSAR & Combinatorial Science, 26 2: 189-203. doi:10.1002/qsar.200530184 67   7 Cited 8 times in Scopus8 0
Malde, Alpeshkumar, Khedkar, Santosh, Coutinho, Evans and Saran, Anil (2005) Geometry, transition states, and vibrational spectra of boron isostere of N-methylacetamide by ab initio calculations. International Journal of Quantum Chemistry, 102 5: 734-742. doi:10.1002/qua.20446 43   6 Cited 6 times in Scopus6 0
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2007) Inhibition of methionine S-adenosyltransferase of M. smegmatis and M. tuberculosis: homology modeling, docking and de novo inhibitor design. Internet Electronic Journal of Molecular Design, 6 6: 151-166. 70   Cited 0 times in Scopus0
Khedkar, S. A., Malde, A. K. and Coutinho, E. C. (2006) In silico screening of ligand databases: Methods and applications. Indian Journal of Pharmaceutical Sciences, 68 6: 689-696. doi:10.4103/0250-474X.30998 56   Cited 4 times in Scopus4 0
Jadhav, Ganesh S., Patel, Ashok R., Vavia, Pradeep R., Malde, Alpeshkumar K. and Coutinho, Evans C. (2005). Interaction of Valdecoxib with Beta Cyclodextrin: Experimental and Molecular Modeling Studies. In: Journal of Inclusion Phenomenon and Macrocyclic Chemistry: Proceedings of the 3rd Asian Cyclodextrin Conference (ACC2005). 3rd Asian Cyclodextrin Conference (ACC2005), Tianjin, China, (261-273). 8-12 May, 2005. doi:10.1007/s10847-006-9093-2 115   6 Cited 7 times in Scopus7 0
Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho, Evans C. (2007) Isosteres of peptides: boron analogs as dipolar forms of -amino acids - a theoretical study. Journal of Physical Organic Chemistry, 20 2: 151-160. doi:10.1002/poc.1139 74   4 Cited 4 times in Scopus4 0
Verma, Jitender, Malde, Alpeshkumar, Khedkar, Santosh, Iyer, Radhakrishnan and Coutinho, Evans (2009) Local indices for similarity analysis (LISA)-A 3D-QSAR formalism based on local molecular similarity. Journal of Chemical Information and Modeling, 49 12: 2695-2707. doi:10.1021/ci900224u 71   4 Cited 4 times in Scopus4 0
Nair, Pramod C., Malde, Alpeshkumar K., Drinkwater, Nyssa and Mark, Alan E. (2012) Missing fragments: Detecting cooperative binding in fragment-based drug design. ACS Medicinal Chemistry Letters, 3 4: 322-326. doi:10.1021/ml300015u 111   6 Cited 5 times in Scopus5 1
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2005) Modeling human neurokinin-1 receptor structure using the crystal structure of bovine rhodopsin. Internet Electronic Journal of Molecular Design, 4 5: 329-341. 102  
Seviour, Thomas, Malde, Alpeshkumar K., Kjelleberg, Staffan, Yuan, Zhiguo and Mark, Alan E. (2012) Molecular dynamics unlocks atomic level self-assembly of the exopolysaccharide matrix of water-treatment granular biofilms. Biomacromolecules, 13 6: 1965-1972. doi:10.1021/bm3005808 105   9 Cited 10 times in Scopus10 0
Khedkar, S. A., Malde, A. K., Coutinho, E. C. and Srivastava, S. (2007) Pharmacophore Modeling in Drug Discovery and Development: An Overview. Medicinal Chemistry, 3 2: 187-197. doi:10.2174/157340607780059521 98   37 Cited 45 times in Scopus45 0
Hoang, Huy N., Driver, Russell W., Beyer, Renée L., Malde, Alpeshkumar K., Le, Giang T., Abbenante, Giovanni, Mark, Alan E. and Fairlie, David P. (2011) Protein a-turns recreated in structurally stable small molecules. Angewandte Chemie International Edition, 123 47: 11303-11307. doi:10.1002/ange.201105119 116   7 Cited 7 times in Scopus7 0
Prabhu, Arati, Malde, Alpehskumar, Coutinho, Evans and Srivastava, Sudha (2005) Solution conformation of Substance P antagonists—[d-Arg1, d-Trp7,9, Leu11]-SP, [d-Arg1, d-Pro2, d-Trp7,9, Leu11]-SP and [d-Pro2, d-Trp7,9]-SP by CD, NMR and MD simulations. Peptides, 26 5: 875-885. doi:10.1016/j.peptides.2004.12.001 39   5 Cited 6 times in Scopus6 0
Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho, Evans C. (2006) Stationary Points on the PES of N-Methoxy Peptides and Their Boron Isosteres: An Ab Initio Study. Journal of Chemical Theory and Computation, 2 6: 1664-1674. doi:10.1021/ct600192g 81   6 Cited 5 times in Scopus5 0
Pal, Manojit, Madan, Manjula, Padakanti, Srinivas, Pattabiraman, Vijaya R., Kalleda, Srinivas, Vanguri, Akhila, Mullangi, Ramesh, Mamidi, N. V. S. Rao, Casturi, Seshagiri R., Malde, Alpeshkumar, Gopalakrishnan, B. and Yeleswarapu Koteswar R. (2003) Synthesis and Cyclooxygenase-2 Inhibiting Property of 1,5-Diarylpyrazoles with Substituted Benzenesulfonamide Moiety as Pharmacophore: Preparation of Sodium Salt for Injectable Formulation. Journal of Medicinal Chemistry, 46 19: 3975-3984. doi:10.1021/jm020563g 96   41 Cited 41 times in Scopus41 0
Mittal, Shilpi, Malde, A. K., Selvan, C., Arun, K. H. S., Johar, P. S., Jachak, Sanjay M., Ramarao, P., Bharatam, P. V. and Chawla, H. P. S. (2004) Synthesis and evaluation of S-4-(3-thienyl)phenyl-α-methylacetic acid. Bioorganic & Medicinal Chemistry Letters, 14 4: 979-982. doi:10.1016/j.bmcl.2003.11.066 37   6 Cited 9 times in Scopus9 0
Manvar, Atul, Malde, Alpeshkumar, Verma, Jitender, Virsodia, Vijay, Mishra, Arun, Upadhyay, Kuldip, Acharya, Hrishikesh, Coutinho, Evans and Shah, Anamik (2008) Synthesis, anti-tubercular activity and 3D-QSAR study of coumarin-4-acetic acid benzylidene hydrazides. European Journal of Medicinal Chemistry, 43 11: 2395-2403. doi:10.1016/j.ejmech.2008.01.016 63   36 Cited 37 times in Scopus37 0
Nayyara, Amit, Mongaa, Vikramdeep, Maldeb, Alpeshkumar, Coutinhob, Evans and Jaina, Rahul (2007) Synthesis, anti-tuberculosis activity, and 3D-QSAR study of 4-(adamantan-1-yl)-2-substituted quinolines. Bioorganic & medicinal chemistry, 15 2: 626-640. doi:10.1016/j.bmc.2006.10.064 102   65 Cited 77 times in Scopus77 0
Nayyar, Amit, Malde, Alpeshkumarb, Coutinhob, Evans and Jain, Rahul (2006) Synthesis, anti-tuberculosis activity, and 3D-QSAR study of ring-substituted-2/4-quinolinecarbaldehyde derivatives. Bioorganic & medicinal chemistry, 14 21: 7302-7310. doi:10.1016/j.bmc.2006.06.049 94   37 Cited 43 times in Scopus43 1
Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2014) Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. Journal of Computer-Aided Molecular Design, 28 3: 221-233. doi:10.1007/s10822-014-9713-7 87   4 Cited 4 times in Scopus4 0
Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho, Evans C. (2007) The B(OH)−NH Analog Is a Surrogate for the Amide Bond (CO−NH) in Peptides: An ab Initio Study. Journal of Chemical Theory and Computation, 3 2: 619-627. doi:10.1021/ct600256s 71   3 Cited 3 times in Scopus3 0
Malde, Alpeshkumar K., Khedkar, Santosh A. and Coutinho, Evans C. (2006) The ω, phi, and ψ Space of N-Hydroxy-N-methylacetamide and N-Acetyl-N ‘-hydroxy-N ‘-methylamide of Alanine and Their Boron Isosteres. Journal of Chemical Theory and Computation, 2 2: 312-321. doi:10.1021/ct050242v 86   5 Cited 5 times in Scopus5 0
Khedkar, Santosh A., Malde, Alpeshkumar K. and Coutinho, Evans C. (2006) Topology of human methionine S-adenosyltransferase. Indian Journal of Chemistry A, 45A 1: 138-145. 120   0 Cited 0 times in Scopus0
Malde, Alpeshkumar K., Srivastava, Sudha S. and Coutinho, Evans C. (2007) Understanding interactions of gastric inhibitory polypeptide (GIP) with its G-protein coupled receptor through NMR and molecular modeling. Journal of Peptide Science, 13 5: 287-300. doi:10.1002/psc.839 67   11 Cited 8 times in Scopus8 0
Nair, Pramod C., Malde, Alpeshkumar K. and Mark, Alan E. (2011) Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT). Journal of Chemical Theory and Computation, 7 5: 1458-1468. doi:10.1021/ct1007229 119   4 Cited 4 times in Scopus4 0