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| Research Publications |
| 101. |
DreamWeb: An Online Tool for Graph-Based Modeling of NMR Protein Structure.
Niladri Ranjan Das, Kunal Narayan Chaudhury, and
Debnath Pal.
Proteomics, , IN PRESS (2024). DOI: 10.1002/pmic.202300379
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| 100. |
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
Shantanu Jain, Constantina Bakolitsa, Steven E. Brenner, Predrag Radivojac, ...
Debnath Pal et al.
Genome Biology, 25:53, 1-46 (2024). DOI: 10.1186/s13059-023-03113-6
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| 99. |
Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches.
Swati Gupta, and
Debnath Pal.
Journal of Biomolecular Structure and Dynamics, 1-11 (2024). DOI:10.1080/07391102.2024.2325107
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| 98. |
Identification of Potential Oral Cancer Drugs as Bcl-2 Inhibitors from Known Anti-Neoplastic Agents Through Docking Studies.
Chandan Raychaudhury, Shreyaa Srinivasan, and
Debnath Pal.
Journal of Mathematical Chemistry (Special issue “Recent Advances in Mathematical and Theoretical Chemistry), 62317-329 (2024). DOI:10.1007/s10910-023-01537-w
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| 97. |
Dynamics of a single-strain and two-strain respiratory infectiondriven by travel on a metapopulation network.
Indrajit Ghosh, Sk Shahid Nadim, Soumyendu and
Debnath Pal.
Nonlinear Dynamics, 111, 21371-21389 (2023). DOI:10.1007/s11071-023-08952-3
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| 96. |
INTERPIN: a repository for intrinsic transcription termination hairpins in bacteria.
Swati Gupta, Namrata Padmashali and
Debnath Pal.
Biochemie, 214B, 228-236 (2023). DOI:10.1016/j.biochi.2023.07.018
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| 95. |
Intrinsic Proclivity of Left-Handed Conformation in Large Nest Motif Peptides Inferred from Molecular Dynamics.
Subhankar Sahu, Raja Banerjee and
Debnath Pal.
Journal of Biomolecular Structure and Dynamics, IN PRESS (2023). DOI:10.1080/07391102.2023.2236710
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| 94. |
A Pathway Model of Glucose-Stimulated Insulin Secretion in the Pancreatic Cell.
Deepa Maheshvare M., Soumyendu Raha, Matthias König and
Debnath Pal.
Frontiers in Endocrinology - Systems Endocrinology, IN PRESS (2023). DOI: 10.3389%2Ffendo.2023.1185656
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| 93. |
Quaternary structure analysis of IRE1.
Samirul Bashir,
Debnath Pal
, Ozaira Qadri, Mariam Banday, and Khalid Fazili.
MicroPubl Biol., 1-3 (2023). DOI: 10.17912/micropub.biology.000763
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| 92. |
The Bcl-2 family protein Bid interacts with the ER stress sensor IRE1 to differentially modulate its RNase activity.
Samirul Bashir, Mariam Banday, Ozaira Qadri,
Debnath Pal
, Arif Bashir, Nazia Hilal, Mohammad Altaf and Khalid Majid Fazili.
FEBS Letters, (2023). DOI: 10.1002/1873-3468.14593
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| 91. |
Proline-Proline dyad in the Fusion Peptide in the S2 Domain of the Spike Protein of Murine β–Coronaviruses Synchronizes Differential Neuroglial Tropism in the CNS.
Abass Alao Safiriyu, Vaishali Mulchandani, Mohammed Nahaf Anakkacheri,
Debnath Pal
, Jayasri Das Sarma.
Viruses, 15:215, 1-30 (2023). DOI: 10.3390/v15010215
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| 90. |
Investigation of protein-ligand binding motions through protein conformational morphing and clustering of cytochrome bc1-aa3 super complex.
Sindhs Thangaraj, Rajamanikandan Sundaraj, Jeyakanthan Jeyaraman and
Debnath Pal
. Journal of Molecular Graphics and Modelling, 118:108347, 1-8 (2023). DOI: 10.1016/j.jmgm.2022.108347
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| 89. |
Improved NMR-data-compliant protein structure modeling captures context-dependent variations and expands the scope of functional inference.
Niladri Ranjan Das, Kunal Narayan Chaudhury and
Debnath Pal
Proteins: Structure, Function, and Bioinformatics. 91 412-435 (2023). DOI: 10.1002/prot.26439
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| 88. |
Molecular spectroscopic and docking analysis of the interaction of fluorescent thiadicarbocyanine dye with biomolecule bovine serum albumin.
Umesha Katrahalli, Shanker Govindaswamy,
Debnath Pal
, Manjunatha DH.
Journal of Biomolecular Structure and Dynamics, 1-11 (2022). DOI: 10.1080/07391102.2022.2158135
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| 87. |
MD DaVis: Interactive Data Visualization of Protein Molecular Dynamics.
Dibyajyoti Maity and
Debnath Pal
. Bioinformatics, 38, 3299-3301 (2022). DOI: 10.1093/bioinformatics/btac314
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| 86. |
Two consecutive prolines in the fusion peptide of murine β-coronavirus Spike protein predominantly determine fusogenicity and may be essential but not sufficient to cause demyelination.
Abass Alao Safiriyu, Manmeet Singh, Abhinoy Kishore, Vaishali Mulchandani, Dibyajyoti Maity, Amrutamaya Behera, Bidisha Sinha,
Debnath Pal
, Jayasri Das Sarma
. Viruses, 14:834 1-27 (2022). DOI: 10.3390/v14040834
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| 85. |
Somatic mutation analyses of stem-like cells in gingivobuccal oral squamous cell carcinoma reveals DNA damage response genes.
Sachendra Kumar, Annapoorni Rangarajan, and
Debnath Pal
. Genomics, 114:110308 1-10 (2022). DOI: 10.1016/j.ygeno.2022.110308
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| 84. |
Azadirachta indica A. Juss bark extract and its Nimbin isomers restrict β-coronaviral infection and replication.
Lucky Sarkar, Lauren Oko, Soham Gupta, Andrew Bubak, Bishnu Das, Parna Gupta, Abass Alao Safiriyu, Chirag Singhal, Ujjwal Neogi, David Bloom, Arup Banerjee, Ravi Mahalingam, Randall Cohrs, Michael Koval, Kenneth S. Shindler,
Debnath Pal
, Maria Nagel, and Jayasri Das Sarma.
Virology, 569 13-28 (2022). DOI: 10.1016/j.virol.2022.01.002
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| 83. |
A graph-based framework for multi-scale modeling of physiological transport.
Deepa Maheshvare M., Soumyendu Raha and
Debnath Pal
. Frontiers in Network Physiology, 1, ISSN=2674-0109 (2022). DOI:10.3389/fnetp.2021.802881 BIORXIV
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| 82. |
Network-based identification of miRNAs and transcription factors and in silico drug screening targeting δ-secretase involved in Alzheimer’s disease.
Saleem Iqbal, Md. Zubbair Malik and
Debnath Pal
. Heliyon, 7:e08502, 1-11 (2021). DOI: 10.1016/j.heliyon.2021.e08502
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| 81. |
Sustained AMPK activation and proline metabolism play critical roles in the survival of matrix-deprived transformed cells.
Manipa Saha, Neha Deshpande, Abhinav Dubey,
Debnath Pal
, Hanudatta S. Atreya and Annapoorni Rangarajan
. Frontiers in Cell and Developmental Biology, 9:771366, 1-12 (2021). DOI: 10.3389/fcell.2021.771366
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| 80. |
Molecular Dynamics of Hemoglobin Reveals Structural Alterations and Explains the Interactions Driving Sickle Cell Fibrillation.
Dibyajyoti Maity and
Debnath Pal
. The Journal of Physical Chemistry B, 125, 9921-9933 (2021). DOI: 10.1021/acs.jpcb.1c01684
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| 79. |
Cytochrome bc1-aa3 oxidase supercomplex as emerging and potential drug target against tuberculosis.
Sindhu Thangaraj and
Debnath Pal
. Current Molecular Pharmacology, 15380-392 (2022). DOI: 10.2174/1874467214666210928152512
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| 78. |
DJ-1-Nrf2 axis is activated upon murine β-coronavirus infection in the CNS.
Soumya Kundu, Fareeha Saadi, Sourodip Sengupta, Gisha Rose Antony, Vineeth A. Raveendran, Rahul Kumar, Mithila Ashok Kamble, Lucky Sarkar, Amy Burrows,
Debnath Pal
, Ganes C. Sen, and Jayasri Das Sarma
. Journal of Brain Disorders, 4:100021, 1-10 (2021). DOI: 10.1016/j.dscb.2021.100021
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| 77. |
Clusters of hairpins induce intrinsic transcription termination in bacteria.
Swati Gupta and
Debnath Pal
. Scientific Reports, 11:16194, 1-18 (2021). DOI: 10.1038/s41598-021-95435-3
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| 76. |
Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates.
Rajnandani Kashyap, Naga Veera Yerra, Joachyutharayalu Oja, Sandeepchowdary Bala, Gal Reddy Potuganti, Jagadeshwar Reddy Thota, Manjula Alla,
Debnath Pal
and Anthony Addlagatta
. Communications Chemistry, 4:113, 1-9 (2021). DOI: 10.1038/s42004-021-00552-9
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| 75. |
A computational framework for modeling functional protein-protein interactions.
Abantika Pal,
Debnath Pal
and Pralay Mitra
. Protein: Structure, Function, and Bioinformatics, 89, 1353-1364 (2021). DOI:10.1002/prot.26156
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| 74. |
Inferring Metal Binding Sites in Flexible Regions of Proteins.
Aditi Garg and
Debnath Pal
. Protein: Structure, Function, and Bioinformatics, 89, 1125-1133 (2021). DOI: 10.1002/prot.26085
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| 73. |
Spike glycoprotein is central to Coronavirus pathogenesis - parallel between m-CoV and SARS-CoV-2.
Fareeha Saadi,
Debnath Pal
and Jayasri Das Sarma.
Annals of Neurosciences, 1023755, 1-17 (2021). DOI: 10.1177/09727531211023755
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| 72. |
Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity.
Debnath Pal.
Journal of Structural Biology, 213:107713, 1-10 (2021). DOI: 10.1016/j.jsb.2021.107713 BioaRxiv
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| 71. |
New Facets of Larger Nest Motifs in Proteins.
Debnath Pal,
Subhankar Sahu and Raja Banerjee.
Proteins: Structure, Function, and Bioinformatics, 88, 1413-1422 (2020). DOI: 10.1002/prot.25961
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| 70. |
Aggregation of M3 (E376D) variant of alpha1 antitrypsin.
Arif Bashir, Younis Hazari,
Debnath Pal,
Dibyajyoti Maity, Samirul Bashir, Laishram Singh, Naveed Shah and Khalid Fazili
. Scientific Reports, 10:8290, 1-13 (2020). DOI:10.1038/s41598-020-64860-1
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| 69. |
Usefulness of Graph Vertex Complexity and Class Partial Information Content in Explaining Gas Phase Thermal Entropy of Chemical Compounds.
Chandan Raychaudhury and
Debnath Pal
. Journal of Mathematical Chemistry, 51, 2718-2730 (2020). DOI: 10.1007/s10910-020-01118-1
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| 68. |
Towards Accelerated Genome Informatics on Parallel HPC Platforms: The ReneGENE-GI Perspective.
Santhi Natarajan,
Krishnakuman N.,
Debnath Pal
and S. K. Nandy.
Journal of Signal Processing Systems, 92, 1197-1213 (2020). DOI:10.1007/s11265-019-01452-x
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| 67. |
Structural analysis of glutathionyl hemoglobin using native mass spectrometry.
Monita Muralidharan, Amrita Mitra, Dibyajyoti Maity,
Debnath Pal,
Amit K. Mandal.
Journal of Structural Biology, 208:107386, 1-8 (2019). DOI: 10.1016/j.jsb.2019.09.003
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| 66. |
Assessing predictions on fitness effects of missense variants in calmodulin.
Jing Zhang, Lisa N. Kinch, Qian Cong, Panagiotis Katsonis, Olivier Lichtarge, Emidio Capriotti, Rita Casadio,
Debnath Pal
, Jochen Weile, Song Sun, Atina G Cote, Frederick P. Roth and Nick V. Grishin.
Human Mutation Variation, Informatics, and Disease, 40, 1463-1473 (2019). DOI:10.1002/humu.23857
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| 65. |
Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.
Alin Voskanian, Panagiotis Katsonis, Olivier Lichtarge, Vikas Pejaver, Predrag Radivojac, Sean D. Mooney, Emidio Capriotti, Yana Bromberg, Yanran Wang, Max Miller, Pier Luigi Martelli, Castrense Savojardo, Giulia Babbi, Rita Casadio, Yue Cao, Yuanfei Sun, Yang Shen, Aditi Garg,
Debnath Pal
, Yao Yu, Chad D. Huff, Sean V. Tavtigian, Erin Young, Susan L. Neuhausen, Elad Ziv, Lipika R. Pal, Gaia Andreoletti, Steven Brenner, John Moult, Maricel G. Kann.
Human Mutation Variation, Informatics, and Disease, 40, 1612-1622 (2019). DOI:10.1002/humu.23849
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| 64. |
Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge.
Castrense Savojardo, Maria Petrosino, Giulia Babbi, Samuele Bovo, Carles Corbi-Verge, Rita Casadio, Piero Fariselli, Lukas Folkman, Aditi Garg, Mostafa Karimi, Panagiotis Katsonis, Philip M. Kim, Olivier Lichtarge, Pier Luigi Martelli, Alessandra Pasquo,
Debnath Pal
, Yang Shen, Alexey V. Strokach, Paola Turina, Yaoqi Zhou, Gaia Andreoletti, Roberta Chiaraluce, Valerio Consalvi and Emidio Capriotti.
Human Mutation Variation, Informatics, and Disease, 40, 1392-1399 (2019). DOI:10.1002/humu.23843
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| 63. |
Predicting Gas Phase Entropy of Select Hydrocarbon Classes Through Specific Information Theoretical Molecular Descriptors.
Chandan Raychaudhury,
Md. Imbesat Hassan Rizvi and
Debnath Pal.
SAR and QSAR in Environmental Research, 30, 491-505 (2019). DOI: 10.1080/1062936X.2019.1624613
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| 62. |
Exploring the use of molecular dynamics in assessing protein variants for phenotypic alterations.
Aditi Garg and
Debnath Pal.
Human Mutation Variation, Informatics, and Disease, 40, 1424-1435 (2019). DOI: 10.1002/humu.23800
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| 61. |
A proline insertion-deletion in the spike glycoprotein fusion peptide of mouse hepatitis virus strongly alters neuropathology.
Manmeet Singh,
Abhinoy Kishore,
Dibyajyoti Maity,
Punnepalli Sunanda,
Bankala Krishnarjuna,
Sreeparna Vappala,
Srinivasarao Raghothama,
Lawrence C. Kenyon,
Debnath Pal
and Jayasri Das Sarma.
Journal of Biological Chemistry, 294, 8064-8087 (2019). DOI: 10.1074/jbc.RA118.004418
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| 60. |
Serum biomarkers identification by iTRAQ and verification by MRM: S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in glioblastoma.
Anjali Arora,
Vikas Patil,
Paramita Kundu,
Patutu Kondaiah,
Alangar S. Hegde,
Arimappamagan Arivazhagan,
Vani Santosh,
Debnath Pal
and Kumaravel Somasundaram.
Scientific Reports, 9:2749, 1-12 (2019). DOI: 10.1038/s41598-019-39067-8
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| 59. |
Interaction of Arsenic with Gap Junction Protein Connexin 43 Alters Gap Junctional Intercellular Communication.
Afaq Hussain,
Subhajit Das Sarma,
Swathy Babu,
Debnath Pal,
and Jayasri Das Sarma.
BBA - Molecular Cell Research, 65, 1423-1436 (2018). DOI: 10.1016/j.bbamcr.2018.07.014.
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| 58. |
Molecular insights of inhibition in sickle hemoglobin polymerization upon glutathionylation: hydrogen/deuterium exchange mass spectrometry and molecular dynamics simulation based approach.
Rajdeep Das,
Amrita Mitra,
Gopa Mitra,
Dibyajyoti Maity,
Vijay Bhat,
Debnath Pal,
Cecil Ross,
Anura V. Kurpad and
Amit Kumar Mandal.
Biochemical Journal, 475, 2153-2166 (2018). DOI: 10.1042/BCJ20180306. Cover Page Article
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| 57. |
Combinatorial Design of Molecule using Activity-Linked Substructural Topological Information as Applied to Antitubercular Compounds.
Chandan Raychaudhury,
Md. Imbesat Hassan Rizvi and
Debnath Pal.
Current Computer Aided Drug Design, 15, 67-81 (2018). DOI: 10.2174/1573409914666180509152711
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| 56. |
Ebolavirus interferon antagonists—protein interaction perspectives to combat pathogenesis.
Anupam Banerjee,
Abantika Pal,
Debnath Pal
and Pralay Mitra.
Briefings in Functional Genomics, 17 , 392-401 (2017). DOI: 10.1093/bfgp/elx034
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| 55. |
Assessment of Adaptive Breast Cancer Screening Policies for Improved Mortality Reduction in Low to Middle Income Countries.
Baban Wagh,
Ramesh Chaluvarayaswamy and
Debnath Pal.
Asian Pacific Journal of Cancer Prevention 18 , 2375-2380 (2017). DOI: 10.22034/APJCP.2017.18.9.2375
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| 54. |
Molecular dynamics information improves cis-peptide based function annotation of proteins.
Sreetama Das,
Pratiti Bhadra,
S. Ramakumar and
Debnath Pal.
Journal of Proteome Research, 16, 2936-2946 (2017). DOI: 10.1021/acs.jproteome.7b00217
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| 53. |
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 40, 1453-1462 (2017). DOI: 10.1007/s00449-017-1803-1
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| 52. |
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
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| 51. |
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:e22921, 1-15 (2017). DOI: 10.1002/bip.22921
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| 50. |
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, 54, 816-825 (2016). DOI: 10.1007/s10528-016-9758-5"
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| 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, 12, 2408-2416 (2016). DOI: 10.1039/C6MB00259E
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| 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
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| 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). DOI: 10.1021/acs.analchem.5b03082
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| 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). DOI: 10.1016/j.ab.2015.07.010
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| 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). DOI: 10.1021/acs.analchem.5b00990
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| 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). DOI: 10.1111/febs.13100
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| 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). DOI: 10.1007/s12038-014-9453-9; PDF Supplementary Material
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| 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). DOI: 10.1002/prot.24609
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| 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
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| 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). DOI: 10.5562/cca2306 (Invited article on the occasion of 70th birthday of Prof. Douglas J. Klein) PDF
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| 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). DOI: 10.1007/s10910-013-0233-9
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| 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). DOI: 10.2174/157340912800492410
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| 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). DOI: https://doi.org/10.1093/nar/gkr317
PDF
PRUNE PROBE
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| 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). DOI: 10.1016/j.str.2011.01.009
Link
IPAC, Among
Top 10 Downloads
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| 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). DOI: https://doi.org/10.1093/nar/gkq971
PDF
WebGeSTer and WebGeSTer DB
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| 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). DOI: 10.1002/jcc.21657
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). DOI: 10.1007/s00894-010-0758-9
Link
DockYard Server
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| 32. |
New measures for estimating surface complementarity and packing
at protein-protein interfaces.
Pralay Mitra and
Debnath Pal.
FEBS Letters 584, 1163-1168 (2010). DOI: 10.1016/j.febslet.2010.02.021
Link
Download Software
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| 31. |
Interface of apoptotic protein complexes has distinct properties.
Pralay Mitra,
Riddhiman Dhar and
Debnath Pal.
In Silico Biol. 9, 365-378 (2009). DOI: 10.3233/ISB-2009-0411
Link or PDF
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| 30. |
Inferring molecular function: contributions from functional linkages.
Arturo Medrano-Soto,
Debnath Pal
and David Eisenberg.
Trends in Genetics 24, 587-590 (2008). DOI: 10.1016/j.tig.2008.10.001
Link
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| 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, 1-18 (2008). DOI: 10.1186/gb-2008-9-3-r52
PDF | Cover Page
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| 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). DOI: 10.1021/bi701078v
Link
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| 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). DOI: 10.1016/j.str.2007.06.021
Link
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| 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). DOI: 10.1016/j.str.2004.10.015 (http://proknow.mbi.ucla.edu/) (Focus Article) (Among Top 20 Downloads at Structure until April 2005)
PDF
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| 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). DOI: 10.1093/protein/gzh093
PDF
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| 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). DOI: 10.1002/anie.200290009
PDF
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| 22. |
Secondary structures at polypeptide-chain termini and their features. Rajasri Bhattacharyya,
Debnath Pal
and Pinak Chakrabarti.
Acta Crystallographica D 58, 1793-1802(2002). DOI: 10.1107/S0907444902013069
PDF
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| 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). DOI: 10.1107/S0907444902014610
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| 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). DOI: 10.1039/B101476P
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| 19. |
On residues in the the disallowed region of the Ramachandran map.
Debnath Pal
and Pinak Chakrabarti.
Biopolymers 63, 195-206 (2002). DOI: 10.1002/bip.10051
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| 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). DOI: 10.1021/bi015677t
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| 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). DOI: 10.1016/S0968-0004(01)01935-1
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| 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). DOI: 10.1080/07391102.2001.10506725
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Fig2a and Fig2b
Fig2c
Fig2d
Fig4a
Fig6a and Fig6b
Fig6c
Fig6d
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| 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). DOI: 10.1016/S0079-6107(01)00005-0
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| 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). DOI: 10.1080/07391102.2000.10506665
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| 13. |
b-sheet propensity and its correlation with parameters based on conformation.
Debnath Pal
and Pinak Chakrabarti.
Acta Crystallographica D56, 589-594 (2000). DOI: 10.1107/S090744490000367X
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| 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). DOI: 10.1016/S0039-128X(99)00097-5
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| 11. |
Terminal residues in protein chains: residue preference and conformation.
Debnath Pal
and Pinak Chakrabarti.
Biopolymers 53, 467-475 (2000). DOI: 10.1002/(SICI)1097-0282(200005)53:6<467::AID-BIP3>3.0.CO;2-9
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| 10. |
Environment of tryptophan side chains in proteins. Uttamkumar Samanta,
Debnath Pal
and Pinak Chakrabarti.
Proteins: Structure, Function and Genetics 38, 288-300 (2000). DOI: 10.1002/(SICI)1097-0134(20000215)38:3<288::AID-PROT5>3.0.CO;2-7
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| 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). DOI: 10.1006/jmbi.1999.3217
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| 8. |
Packing of aromatic rings against tryptophan residues in proteins. Uttamkumar Samanta,
Debnath Pal
and Pinak Chakrabarti.
Acta Crystallographica D55, 1421-1427 (1999). DOI: https://doi.org/10.1107/S090744499900726X
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| 7. |
Graphical representation of salient conformational features of protein residues.
Debnath Pal
and Pinak Chakrabarti.
Protein Engineering 12, 523-526 (1999). DOI: 10.1093/protein/12.7.523
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| 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). DOI: https://doi.org/10.1002/(SICI)1097-0134(19990815)36:3<332::AID-PROT7>3.0.CO;2-H
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| 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). DOI: 10.1093/protein/11.8.631
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| 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). DOI: 10.1080/07391102.1998.10509001
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| 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). DOI: 10.1002/hlca.19970800805
|
| 2. |
An electrophile-nucleophile interaction in metalloprotein structures. Pinak Chakrabarti and
Debnath Pal
.
Protein Science 6, 851-859 (1997). DOI: 10.1002/pro.5560060412
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| 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). DOI: 10.1021/jo961353c
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