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Publications / Informatics & Analytics

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Informatics & Analytics

Tracking 20 Years of Compound-to-Target Output from Literature and Patents
Christopher Southan, Peter Varkonyi, Kiran Boppana, Sarma A. R. P. Jagarlapudi, Sorel Muresan
PLoS ONE 2013, 8(10): e77142

Discovery of novel InhA reductase inhibitors:Application of pharmacophore- and shape-based screening approach
Uday Chandra Kumar, Suneel Kumar BVS, Shaik Mahmood, Sriram D, Prashanta, Kumar-Sahu, Sridevi Pulakanam, Lluís Ballell, Daniel Alvarez-Gomez, Siddharth Malik and Sarma JARP
Future Med. Chem. 2013, 5(3), 249–259

Fibroblast Growth Factor Receptor Inhibitors
Kumar B.V.S, Suneel; Narasu, Lakshmi; Gundla, Rambabu; Dayam, Raveendra; J.A.R.P, Sarma
Current Pharmaceutical Design, 2013, 19(4), 687-701

 

Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies
Sukesh Kalva, S Vadivelan, Ramadevi Sanam, Sarma ARP Jagarlapudi, Lilly M Saleena
Bioinformation 2012, 8(7), 301-8

 

3D-QSAR studies on pyrido[2,3-d]pyrimidine derivatives as fibroblast growth factor receptor 1 inhibitors: application of molecular field analysis (MFA)
Suneel Kumar, B. V. S.; Sarma, Jagarlapudi A. R. P.; Narasu, Lakshmi
International Journal of Drug Design and Discovery 2011, 2(4), 619-632

A Three-Dimensional Pharmacophore Modeling of ITK Inhibitors and virtual screening for novel inhibitors
Vikas Bagga, Om Silakaria, Vijay Singh Ghorela, Gundla Rambabu, Jagarlapudi A.R.P. Sarma
SAR QSAR Environ Res. 2011, (1-2), 171-90

Virtual screening studies on HIV-1 reverse transcriptase inhibitors to design potent leads
S. Vadivelan, T.N. Deeksha, S. Arun, Pavan Kumar Machiraju, Rambabu Gundla, Barij Nayan Sinha, Sarma A.R.P. Jagarlapudi
European Journal of Medicinal Chemistry, 2011

Ligand-based and structure-based approaches in identifying ideal pharmacophore against c-Jun N-terminal kinase-3
Suneel Kumar B.V.S, Rohith Kotla, Revanth Buddiga, Jyoti Roy, Muttineni Ravikumar, Rambabu Gundla, Jagarlapudi A. R. P. Sarma
J. Mol. Model., 2011

Evolution of the physicochemical properties of marketed drugs: can history foretell the future?
Bernard Faller, Giorgio Ottaviani, Peter Ertl, Giuliano Berellini and Alan Collis
Drug Discovery Today, 2011

The influence of the ‘organizational factor’ on compound quality in drug discovery
Paul D. Leeson, Stephen A.St-Gallay
Drug Discovery,2011

Molecular clinical safety intelligence: a system for bridging clinically focused safety knowledge to early-stage drug discovery – the GSK experience
Dana E. Vanderwall, Nancy Yuen, Mohammad Al-Ansari, James Bailey, David Fram, Darren V.S. Green, Stephen Pickett, Giovanni Vitulli, Juan I. Luengo, June S. Almenoff
Drug Discovery Today,2011

What Do Medicinal Chemists Actually Make? A 50-Year Retrospective
Walters WP, Green J, Weiss JR, Murcko MA.
Journal Of Medicinal Chemistry,2011

Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds
Southan C, Boppana K, Jagarlapudi SA, Muresan S.
Journal of Cheminformatics,2011

 

Modelling of Human Caspase-3 protein and docking studies of Caspase-4 inhibitors against modeled Caspase-5
Munipalli Haripriya*, Gundla Rambabu and Sarma A.R.P. Jagarlapudi
Journal of Global Pharma Technology. 2010, 2(7), 13-26

Insilico studies on anthrax lethal factor inhibitors: pharmacophore modeling and virtual screening approaches towards designing of novel inhibitors for a killer.
Roy J, Kumar UC, Machiraju PK, Muttineni RK, Kumar B V S S, Gundla R, Dayam R, Sarma JARP.
J. Mol. Graph. Mod,. 2010, 29(2), 256-265

Evolution of Anti Inflammatory Activity of Aqueous Extracts of Syzygium alternifolium
B. Rama Mohan, K. V. S. R. G. Prasad, J. A. R. P. Sharma
International Journal of Pharmaceutical Sciences,. 2010, 2(3), 865-870

Analgesic and Inflammatory Activities of Polyherbal preparations on Diabetic Rats
B. Rama Mohan, K. V. S. R. G. Prasad, D. Ranganayakulu, J. A. R. P. Sharma
International Journal of Pharmaceutical Sciences,. 2010, 2(3), 892-903

Hypoglycemic and antihyperglycemic Activity of Syzygium Alternifolium (WT.) Walp., Leaf Extracts in normal and diabetic rats
A. Rama Mohan, K. V. S. R. G. Prasad, J. A. R. P. Sharma
International Journal of Drug Development & Researc, 2010, 2(1), 27-32

Combined pharmacophore and structure-guided studies to identify diverse HSP90 inhibitors
Ramadevi Sanam, Sunita Tajne, Rambabu Gundla, S Vadivelan, Pavan kumar Machiraju, Raveendra Dayam, Lakshmi Narasu, Sarma A. R. P. Jagarlapudi, Nouri Neamati
J. Mol. Graph. Mod., 2010

Are There Differences between Launched Drugs, Clinical Candidates, and Commercially Available Compounds?
Kazuki Ohno, Yuichi Nagahara, Kazuhisa Tsunoyama, and Masaya Orita
Journal of Chemical Information and Modeling,2010

Discovery of potential ZAP-70 kinase inhibitors: Pharmacophore design, database screening and docking studies
Ramadevi Sanam, S. Vadivelan, Sunita Tajne, Lakshmi Narasu, G. Rambabu, Sarma A.R.P. Jagarlapudi
Eur. J. Med. Chem., 2009, 44, 4793-4800

Norfloxacin sesquihydrate
Nittala V. Ravindra, Gopal M. Panpalia and Jagarlapudi A. R. P. Sarma
Acta Crystallographica, 2009, 65E, 4303-4303

Database Systems for Knowledge-based Discovery
Sarma A.R.P.J and K.V. Radha Kishan
Chemogenomics, Methods in Molecular Biology, Humana Press. 2009

Knowledge based identification of MAO-B selective inhibitors using pharmacophore and structure based virtual screening models
Kiran Boppana, P.K. Dubey, Sarma A.R.P. Jagarlapudi, S. Vadivelan, G. Rambabu
Eur. J. Med. Chem., 2009

Fragment and Knowledge based approach to design selective GSK3beta inhibitors using Virtual screening models
S Vadivelan, Barij Nayan Sinha, Sunita Tajne, Sarma A R P Jagarlapudi
Eur. J. Med. Chem., 2009

Novel Chemical Space Exploration via Natural Products
Josefin Rosen, Johan Gottfries, Sorel Muresan, Anders Backlund and Tudor I. Oprea Journal of Medicinal Chemistry,2009

ProSAR: A New Methodology for Combinatorial Library Design
Hongming Chen, Ulf Borjesson, Ola Engkvist, Thierry Kogej, Mats A. Svensson, Niklas Blomberg, Dirk Weigelt, Jeremy N. Burrows, Tim Lange
Journal of Chemical Information and Modeling,2009

Physicochemical property profiles of marketed drugs, clinical candidates and bioactive compounds
Christian Tyrchan, Niklas Blomberg, Ola Engkvist, Thierry Kogej, Sorel Muresan
Bioorganic & Medicinal Chemistry Letters,2009

Gaining Insight into Off‐Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis
Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies, Jeremy L. Jenkins
Journal of Chemical Information and Modeling,2009

Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success
Lovering, Jack Bikker, Christine Humblet
Journal of Medicinal Chemistry,2009

 

Bis(5-oxo-4,5-dihydro-8H-2-azonia-4,8,9-trizabicyclo[4.3.0]nona-2,6,8-triene) sulfate
Ravindra, N.V.; Panpalia, G.M.; Sarma A. R. P. Jagarlapudi
Acta Crystallographica, 2008, 64E, 2411-2411

Discovery of novel small-molecule inhibitors of human epidermal growth factor receptor-2: Combined ligand and target-based approach
Gundla R, Kazemi R, Sanam R, Muttineni R, Sarma JARP, Dayam R, Neamati N.
J. Med. Chem., 2008

Pharmacophore modeling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads
S. Vadivelan; B. N. Sinha; G. Rambabu; Kiran Boppana; Sarma A.R.P Jagarlapudi
J. Mol. Graph. Mod., 2008

Kinase‐likeness and Kinase‐Privileged Fragments: Toward Virtual Polypharmacology
Alex M. Aronov*, Brian McClain, Cameron Stuver Moody and Mark A. Murcko
Journal of Medicinal Chemistry,2008

Visual exploration of structure‐activity relationship using maximum common framework
Sung Jin Cho, Yaxiong Sun
Journal of Computer-Aided Molecular Design,2008

Preparation, characterization and conductivity studies of a nasicon system Ag3-2xTaxAl2-x (PO4)3 (x = 0.6-1.4)
Rambabu, G.; Anantharamulu, N.; Rao, K. Koteswara; Sarma, J. A. R. P.; Vithal, M.
Physica Status Solidi A: Applications and Materials Science, 2007, 204(10), 3454-3462

Virtual Screening studies to design potent CDK2-Cyclin A inhibitors
S. Vadivelan, Barij Nayan Sinha, Sheeba Jem Irudayam, and Sarma A. R. P. Jagarlapudi.,
J. Chem. Inf. Model., 2007, 47, 1526-1535

The influence of drug‐like concepts on decision‐making in medicinal chemistry
Paul D. Leeson, Brian Springthorpe
Nature reviews: drug discovery,2007

Complementarity Between Public and Commercial Databases: New Opportunities in Medicinal Chemistry Informatics
Christopher Southan, Peter Varkonyi and Sorel Muresan
Current Topics in Medicinal Chemistry,2007

Chemogenomic approaches to rational drug design
D Rognan
British Journal of Pharmacology,2007

Outsourcing lead optimization: constant change is here to stay
David E. Clark
Drug Discovery Today,2007

Shape Signatures: speeding up computer aided drug discovery
Peter J. Meek, Zhi Wei Liu, Li Feng Tian, Ching Y. Wang, William J. Welsh, Randy J. Zauhar
Drug Discovery Today,2006

Dependence of Molecular Properties on Proteomic Family for Marketed Oral Drugs
Michal Vieth and Jeffrey J. Sutherland
Journal of Medicinal Chemistry,2006

Ligand Coordinate Analysis of SC-558 from the Active Site to the Surface of COX-2: A Molecular Dynamics Study
K. V. V. M. Sai Ram, G. Rambabu, J. A. R. P. Sarma and G. R. Desiraju
J. Chem. Inf. Model., 2006

A review of synthetic and molecular model study towards fixing up bio-active chiral centre at C28 of Lasonolide-A, an anticancer macrolide: A new chiral pool approach
Kar, Paramita; Rao, B. V.; Sarma, J. A. R. P.; Chowdhury, B.; Nagaiah, K.; Gurjar, M. K.
J Ind Chem Soc., 2005, 82(6), 534-537

Virtual Screening of 4-Anilinoquinazoline Analogues as EGFR Inhibitors: Imporatnce of Hydrogen Bonds in the Evaluation of Poses and Scoring Functions
V. Aparna, G. Rambabu, S. K. Panigrahi, J. A. R. P. Sarma and G. R. Desiraju,
J. Chem. Inf. Model., 2005, 45 (3), 725 -738

Design of EGFR Kinase Inhibitors: A Ligand-Based Approach and Its confirmation with Structure-Based Studies
Aparna Vema, Sunil K. Panigrahi, G. Rambabu, B. Gopalakrishnan, J. A. R. P. Sarma and Gautam R. Desiraju,
Bioorg Med Chem., 2003, 11, 21, 4643- 4653

Searching for a Polymorph: Second Crystal Form of 6-Amino-2-Phenylsulfonylimino-1,2-Dihydropyridine
K. R. J. Ram, R. Boese, J. A. R. P. Sarma, L. S. Reddy, P. Vishweshwar, G. R. Desiraju
Angew Chem. Int. Ed. Engl., 2003, 42. 1963-1967

3D-QSAR studies of some [[1-Aryl( or Benzyl)-1-(benzenesulonamido)methyl] phenyl] alkonoic acid derivatives as Thromboxane A2 Receptor antagonists,
K. V. V. M. Sairam, J. A. R. P. Sarma and G. R. Desiraju
Drug Discovery & Design, 2003, 18, 2-3, 47-51

Computer Aided Design of Selective COX-2 inhibitors: Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA) and Docking Studies of some 1,2-diarylimidazole derivatives
G. R. Desiraju, B. Gopalakrishnan, R. K. R. Jetti, A. Nagarju, D. Raveendra, J. A. R. P. Sarma, M.E.Sobhia, and R. Thilagavathi
J. Med. Chem., 2002, 45 (22), 4847-4857

Analogue Based Design of MMP-13 (Collagenase-3) Inhibitors
J. A. R. P. Sarma, G. Rambabu, K. Srikanth, D. Raveendra, M. Vithal
Bioorganic Medicinal Chemistry Letters, 2002, 12, 19, 2689-2693

The Supramolecular Synthon Approach to Predict Crystal Structures
J. A. R. P. Sarma and G. R. Desiraju
Crystal Growth & Design, 2002, 2, 93-100

NMR study of cyclic peptides with renin inhibitor activity,
A.V.S. Sarma, M. H. V. Ramana Rao, J. A. R. P. Sarma, R. Nagaraj, A.S. Dutta and A.C. Kunwar
J. Biophysical and Biochemical methods, 2002, 51, 27-45

3D-QSAR Studies on new Dibenzyltin (IV) Anti-Cancer Agents by Comparative Molecular Field Analysis (CoMFA)
Purnima M.Samuel, Dick de Vos, Prakash V. Diwan, K. Ravi Kumar, D.Raveendra, J. A. R. P. Sarma, and Sujit Roy.,
Bioorganic Medicinal Chemistry Letters, 2002, 12, 61-64

Microwave assisted synthesis of a,a’-bis(benzylidene)ketones in dry media,
J. S. Yadav, B. V. Subba Reddy, A. Nagaraju, and J. A. R. P. Sarma
Synthetic Commun., 2002, 32, 893 – 896

A novel, shape-selective, zeolite-catalyzed synthesis of calyx(4)pyrroles,
M. Radhakrishna, N. Sreenivas, K. V. Raghavan, S. J. Kulakarni, Sarma, J. A. R. P., and M. Vairamani.,
Chem. Commun., 2001, 2226-2227

Computer aided design of selective COX-2 inhibitors: CoMFA and docking studies of some 3,4-diaryloxazolone derivatives,
G. R. Desiraju, J. A. R. P. Sarma, D. Raveendra, B. Gopalakrishnan, R. Thilagavathi, M. E. Sobhia, and H. S. Subramanya
J. Phys. Org. Chem., 2001, 14, 481-487

Inclusion compounds of tetrakis-(4-nitrophenyl) methane: C-H…O networks, psedopolymorphism and structural transformations
Ram Thaimattam, Xue Feng, J. A. R. P. Sarma, Thomas C. W. Mak, and G. R. Desiraju
J. Amer. Chem. Soc., 2001, 123(19); 4432 – 4445