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Research Publications
55. Molecular dynamics information improves cis-peptide based function annotation of proteins. Sreetama Das, Pratiti Bhadra, S. Ramakumar and Debnath Pal. Journal of Proteome Research , IN PRESS (2017).
54. Numerical Simulation of a Glucose Sensitive Composite Membrane Closed-Loop Insulin Delivery System. Shashi Bajaj Mukherjee, Debabrata Datta, Soumyendu Raha and Debnath Pal. Bioprocess and Biosystems Engineering , IN PRESS (2017). DOI: 10.1007/s00449-017-1803-1
53. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield. Pratiti Bhadra and Debnath Pal. Comput Biol Med. 83, 134-142 (2017). DOI: 10.1016/j.compbiomed.2017.02.009
52. Computational design of model scaffold for anion recognition based on the 'CαNN' motif. Tridip Sheet, Suvankar Ghosh, Debnath Pal and Raja Banerjee. Peptide Science, 108, DOI: 10.1002/bip.22921 (2017)
51. Mass Spectrometry-Based Diagnosis of Hemoglobinopathies: A Potential Tool for the Screening of Genetic Disorder. Rajdeep Das, Gopa Mitra, Boby Mathew, Vijay Bhat, Cecil Ross, Debnath Pal and Amit Mandal. Biochemical Genetics, DOI 10.1007/s10528-016-9758-5, (2016)
50. AccuRA: Accurate Alignment of Short Reads on Scalable Reconfigurable Accelerators. Santhi Natarajan, Krishna Kumar N., Debnath Pal and S. K. Nandy. International Conference on Embedded Computer Systems: Architechtures. MOdelling and Simulation (SAMOS) XVI, Accepted , (2016)
49. Unique Functional Role of C-H...S Hydrogen Bond in Substrate Specificity and Enzyme Catalysis of Type 1 Methionine Aminopeptidase. Ravikumar Reddi, Kiran Singarapu, Debnath Pal and Anthony Addlagatta. Molecular Biosystems, DOI: 10.1039/C6MB00259E, (2016)
48. Bacterial Siderophore Mimicking Iron Complexes as DNA Targeting Antimicrobials. Sunil Kumar Boda, Subhendu Pandit, Aditya Garai, Debnath Pal and Bikramjit Basu. RSC Advances, 6, 39245-39260 (2016) DOI: 10.1039/C6RA02603F
47. Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum. Abhinav Dubey, Annapoorni Rangarajan, Debnath Pal and Hanudatta Sastry Atreya. Analytical Chemistry, 87, 12197-12205 (2015)
46. Mass spectrometry based characterization of Hb Beckman variant in a falsely elevated HbA1c sample. Rajdeep Das, Monita Muralidharan, Gopa Mitra, Vijay Bhat, Boby Mathew, Debnath Pal , Cecil Ross and Amit Mandal. Analytical Biochemistry, 489, 53-58 (2015)
45. A pattern recognition based approach for identifying metabolites in NMR based metabolomics. Abhinav Dubey, Annapoorni Rangarajan, Debnath Pal and Hanudatta Sastry Atreya. Analytical Chemistry, 87, 7148-7155 (2015)
44. Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation. Sreetama Das, Suryanarayanrao Ramakumar and Debnath Pal. FEBS Journal, 281, 5602-5621 (2014)
43. Avoiding acidic region streaking in two-dimensional gel electrophoresis: case study with two bacterial whole cell protein extracts. Arnab Roy, Umesh Varshney and Debnath Pal. Journal of Biosciences, 39, 631-642 (2014) PDF Supplementary Material
42. De novo inference of protein function from coarse-grained dynamics. Pratiti Bhadra and Debnath Pal. Proteins: Structure, Function and Bioinformatics, 82, 2443-2454 (2014)
41. Two New Atom Centered Fragment Descriptors and Scoring Function Enhance Classification of Antibacterial Activity. Durga Datta Kandel, Chandan Raychaudhury and Debnath Pal. Journal of Molecular Modeling, 20, 2164 (2014) DOI: 10.1007/s00894-014-2164-1
40. Role of Vertex Index in Substructure Identification and Activity Prediction: A Study on Antitubercular Activity of a Series of Acid Alkyl Ester Derivatives. Chandan Raychaudhury, Durga Datta Kandel and Debnath Pal. Croatica Chimica Acta, 87, 39-47 (2014) (Invited article on the occasion of 70th birthday of Prof. Douglas J. Klein) PDF
39. Information content of molecular graph and prediction of gas phase thermal entropy of organic compounds. Chandan Raychaudhury and Debnath Pal. Journal of Mathematical Chemistry, 51, 2718-2730 (2013)
38. Use of vertex index in structure-activity analysis and design of molecules. Chandan Raychaudhury and Debnath Pal. Current Computer Aided Drug Design, 8,128-134 (2012)
37. PRUNE and PROBE - two modular web services for protein-protein docking . Pralay Mitra and Debnath Pal. Nucleic Acids Research, 39, W229-W234 (Webserver Issue, 2011) PDF   PRUNE  PROBE
36. Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference. Pralay Mitra and Debnath Pal. Structure 19, 304-312 (2011) Link  IPAC, Among Top 10 Downloads
35. WebGeSTer DB - a transcription terminator database. Anirban Mitra, Anil K. Kesarwani, Debnath Pal and Valakunja Nagaraja. Nucleic Acids Research 39, D129-D135 (Database Issue, 2011) PDF   WebGeSTer and WebGeSTer DB
34. Using correlated parameters for improved ranking of protein-protein docking decoys. Pralay Mitra and Debnath Pal. Journal of Computational Chemistry 32, 787-796 (2011) PDF
33. dockYard - a repository to assist modeling of protein-protein docking. Pralay Mitra and Debnath Pal. Journal of Molecular Modeling 17, 599-606 (2011) Link DockYard Server
32. New measures for estimating surface complementarity and packing at protein-protein interfaces. Pralay Mitra and Debnath Pal. FEBS Letters 584, 1163-1168 (2010) Link   Download Software
31. Interface of apoptotic protein complexes has distinct properties. Pralay Mitra, Riddhiman Dhar and Debnath Pal. In Silico Biol. 9, 365-378 (2009) Link or PDF
30. Inferring molecular function: contributions from functional linkages. Arturo Medrano-Soto, Debnath Pal and David Eisenberg. Trends in Genetics 24, 587-590 (2008) Link
29. Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. K. Manikandan, Debnath Pal, S. Ramakumar, Nathan E Brener, Seetharama Iyenger, Guna Seetharaman. Genome Biology , 9:R52(2008) PDF | Cover Page
28. The Saccharomyces cerevisiae Hop1 protein zinc finger motif binds to the Holliday junction and distorts the DNA structure: implications for Holliday junction migration. Pankaj Tripathy, Debnath Pal and Kalappa Muniyappa. Biochemistry 46, 12530-12542 (2007) Link
27. Functional Linkages can Reveal Protein Complexes for Structure Determination. Sul-Min Kim, Peter M. Bowers, Debnath Pal , Michael Strong, Thomas C. Terwilliger, Markus Kaufmann and David Eisenberg. Structure 15, 1079-1089 (2007). Link
26. On Gene Ontology and Function Annotation. Debnath Pal. Bioinformation 1, 97-98 (2006). PDF
25. Inference of protein function from protein structure. Debnath Pal and David Eisenberg. Structure 13, 121-130 (2005). (http://proknow.mbi.ucla.edu/)(Focus Article)(Among Top 20 Downloads at Structure until April 2005) PDF
24. Disulfide bonds, their stereospecific environment and conservation in protein structures. Rajasri Bhattacharyya, Debnath Pal and Pinak Chakrabarti. Protein Engineering Design and Selection 17, 795-808 (2004). PDF
23. New principles of protein structure: nest, eggs and what next? Debnath Pal , Juergen Suehnel and Manfred S. Weiss. Angewandte Chemie 41, 4663-4665(2002). PDF
22. Secondary structures at polypeptide-chain termini and their features. Rajasri Bhattacharyya, Debnath Pal and Pinak Chakrabarti. Acta Crystallographica D 58, 1793-1802(2002). PDF
21. An overview on 2-methyl-2,4-pentanediol in crystallization and in crystals of biological macromolecules. Kanchan Anand, Debnath Pal and Rolf Hilgenfeld. Proceedings of the ICCBM9 conference, Acta Crystallographica D Supplement 58, 1722-1728 (2002). PDF
20. Silver(I) oxide-silver halide mediated alcoholysis of O-benzoyl-myo-inositol 1,3,5-orthoformates: intramolecular assistance by sulfonyl group. Thoniyot Praveen, Tanya Das, Kana M. Sureshan, Mysore S. Shashidhar, Uttamkumar Samanta, Debnath Pal and Pinak Chakrabarti. Journal of the Chemical Society, Perkin Transactions 2 358-365 (2002). PDF
19. On residues in the the disallowed region of the Ramachandran map. Debnath Pal and Pinak Chakrabarti. Biopolymers 63, 195-206 (2002). PDF
18. Conformational properties of ?-tubulin tail peptide: implications for tail-body interaction. Debnath Pal , Pradip Mahapatra, Tapas Manna, Pinak Chakrabarti, Bhabatarak Bhattacharyya, Anirban Banerjee, Gautam Basu and Siddhartha Roy. Biochemistry 40, 15512-15519 (2001). PDF
17. More hydrogen bonds for the (structural) biologist. Manfred S. Weiss, Maria Brandl, Jurgen S nhel, Debnath Pal and Rolf Hilgenfeld. Trends in Biochemical Sciences 26, 521-523 (2001). PDF
16. Non-hydrogen bond interactions involving the methionine sulfur atom. Debnath Pal and Pinak Chakrabarti. Journal of Biomolecular Structure and Dynamics 19, 115-128 (2001). PDF   Fig2a and Fig2b   Fig2c  Fig2d  Fig4a  Fig6a and Fig6b   Fig6c   Fig6d  
15. Interrelationships of side-chain and main-chain conformations in proteins. Pinak Chakrabarti and Debnath Pal . Progress in Biophysics and Molecular Biology 76, 1-102 (2001). PDF
14. Conformational similarity indices between different residues in proteins and a-helix propensities. Debnath Pal and Pinak Chakrabarti. Journal of Biomolecular Structure and Dynamics 18, 273-280 (2000). PDF
13. b-sheet propensity and its correlation with parameters based on conformation. Debnath Pal and Pinak Chakrabarti. Acta Crystallographica D56, 589-594 (2000). PDF
12. Synthesis of 11b-(4-dimethylaminophenyl)-17b-hydroxy-17a-(3-methyl-1-butynyl)-4,9-estradien-3-one and 11b-(4-acetophenyl)-17b-hydroxy-17a-(3-methyl-1-butynyl)-4,9-estradien-3-one: Two new analogues of mifepristone (RU-486). Braja G. Hazra, Sourav Basu, Vandana S. Pore, Padmaker L. Joshi, Debnath Pal and Pinak Chakrabarti. Steroids 65, 157-162 (2000). PDF
11. Terminal residues in protein chains: residue preference and conformation. Debnath Pal and Pinak Chakrabarti. Biopolymers 53, 467-475 (2000). PDF
10. Environment of tryptophan side chains in proteins. Uttamkumar Samanta, Debnath Pal and Pinak Chakrabarti. Proteins: Structure, Function and Genetics 38, 288-300 (2000). PDF
9. Cis peptide bonds in proteins: residues involved, their conformation, interactions and locations. Debnath Pal and Pinak Chakrabarti. Journal of Molecular Biology 294, 271-288 (1999). PDF
8. Packing of aromatic rings against tryptophan residues in proteins. Uttamkumar Samanta, Debnath Pal and Pinak Chakrabarti. Acta Crystallographica D55, 1421-1427 (1999). PDF
7. Graphical representation of salient conformational features of protein residues. Debnath Pal and Pinak Chakrabarti. Protein Engineering 12, 523-526 (1999). PDF
6. Estimates of the loss of main-chain conformational entropy of different residues on protein folding. Debnath Pal and Pinak Chakrabarti. Proteins: Structure, Function and Genetics 36, 332-339 (1999). PDF
5. Main-chain conformational features at different conformations of the side-chains in proteins. Pinak Chakrabarti and Debnath Pal . Protein Engineering 11, 631-647 (1998). PDF
4. Different types of interactions involving cysteine sulfhydryl group in proteins. Debnath Pal and Pinak Chakrabarti. Journal of Biomolecular Structure and Dynamics 15, 1059-1072 (1998). PDF
3. Push-pull butadienes: Evidence for a possible C-H...S hydrogen bond in 4-(Methylthio)-4-nitro-1-(pyrrolidin-1-yl)-buta-1,3-diene. Sheetal S. Surange, Govindaraj Kumaran, Srinivasachari Rajappa, Debnath Pal and Pinak Chakrabarti. Helv. Chimica Acta 80, 2329-2336 (1997).
2. An electrophile-nucleophile interaction in metalloprotein structures. Pinak Chakrabarti and Debnath Pal . Protein Science 6, 851-859 (1997). PDF
1. Stereodivergent C-C bond formation on arene-chromium template: endo-selective allylation by Hosomi-Sakurai reaction. S. Sur, S. Ganesh, D. Pal , P. Chakrabarti and A. Sarkar. Journal of Organic Chemistry 61, 8362-8363 (1996). PDF
Book Chapters
4. Information Content Measures and Prediction of Physical Entropy of Organic Compounds. Chandan Raychaudhury and Debnath Pal. (2016). Book Chapter in Mathematical Foundations and Applications of Graph Entropy, Edited by M. Dehmer, Z. Chen, X. Li, Y. Shi, edsa,. Wiley-VCH. Link
3. Discrimination of small molecules using topological molecular descriptors. Chandan Raychaudhury and Debnath Pal. (2015). Book Chapter in Advances in Mathematical Chemistry and Applications, Vol. 2, 2015, 55-73; Edited by Basak S. et al., Bentham Science Publishers. Link
2. Microbes: Turning them into allies. Debnath Pal. (2005). Book Chapter in Biotechnological Applications of Microbes. Edited by Gopi K. Podilla and Ajit Verma, IK International Private Limited, New Delhi. Link
1. TB or Not TB: A Structural Genomics Mission? Celia W. Goulding, Debnath Pal and David Eisenberg. (2004). Chapter 11, 165-190 in Tuberculosis and the Tubercle Bacillus. Edited by Stewart T. Cole, Institut Pasteur; Kathleen D. Eisenach, University of Arkansas for Medical Sciences; David N. McMurray, Texas A&M University System Health Science Center; William R. Jacobs, Jr., Albert Einstein College of Medicine. Book ISBN: 1-55581-295-3 Link   PDF
Patents
1. Three applications pending.