Indian Institute of Technology Kharagpur |

Journal

E(Q)AGNN-PPIS: Attention Enhanced Equivariant Graph Neural Network for Protein-Protein Interaction Site Prediction by A., Suvvada R. , Bhowmick P. K., Mitra P. IEEE Transactions on Signal and Information Processing over Networks - (Accepted/In-Press)
Deciphering the Lexicon of Protein Targets: A review on Multifaceted Drug Discovery in the Era of Artificial Intelligence by Nandi S., Bhaduri S. , Das D. , Ghosh P. , Mandal M. , Mitra P. ACS Molecular Pharmaceutics 21 1563-1590 (2024)
The molecular prognostic score, a classifier for risk stratification of high-grade serous ovarian cancer by Sarkar S., Saha S. A., Swarnakar A. , Chakrabarty A. , Dey A. , Sarkar P. , Banerjee S. , Mitra P. Journal of Ovarian Research 17 159- (2024)
MaTPIP: a deep-learning architecture with eXplainable AI for sequence-driven, feature mixed protein-protein interaction prediction by Ghosh S., Mitra P. Computer Methods and Programs in Biomedicine 244 107955- (2024)
A novel computational predictive biological approach distinguishes Integrin 1 as a salient biomarker for breast cancer chemoresistance by Das S., Kundu M., Hassan A., Parekh A., Jena B.C., Mundre S., Banerjee I., Yetirajam R., Das C.K., Pradhan A.K., Das S.K., Emdad L., Mitra P., Fisher P.B., Mandal M. Biochimica et Biophysica Acta - Molecular Basis of Disease 1869 - (2023)
A sequence space search engine for computational protein design to modulate molecular functionality by Malik A., Banerjee A. , Pal A. , Mitra P. Journal of Biomolecular Structure & Dynamics 41 2937-2946 (2023)
Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India by Sarkar P., Banerjee S., Saha S.A., Mitra P., Sarkar S. Scientific Reports 13 - (2023)
Modularity-based Parallel Protein Design Algorithm with an Implementation using Shared Memory Programming by Pal A., Mulumudy R. , Mitra P. PROTEINS: Structure, Function, and Bioinformatics 90 658-669 (2022)
Therapeutic targeting of RBPJ, an upstream regulator of ETV6 gene, abrogates ETV6-NTRK3 fusion gene transformations in glioblastoma by Biswas A., Rajesh Y. , Das S. , Banerjee I. , Kapoor N. , Mitra P. , Mandal M. Cancer Letters 544 215811-215825 (2022)
Human Prion Protein: Exploring the Thermodynamic Stability and Structural Dynamics of its Pathogenic Mutants by Halder P., Mitra P. Journal of Biomolecular Structure & Dynamics 40 11274-11290 (2022)
ProFuMCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell by Das B., Mitra P. Journal of Molecular Modeling 28 167-175 (2022)
Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins by Pal B., Mitra P. Journal of Molecular Biology 433 167149- (2021)
A computational framework for modeling functional protein-protein interactions by Pal A., Pal D. , Mitra P. PROTEINS: Structure, Function, and Bioinformatics 89 1353-1364 (2021)
High-performance Whole-cell Simulation Exploiting Modular Cell Biology Principles by Das B., Mitra P. Journal of Chemical Information and Modeling 61 1481-1492 (2021)
An evolutionary profile guided greedy parallel replica-exchange Monte Carlo search algorithm for rapid convergence in protein design by Banerjee A., Pal K. , Mitra P. IEEE/ACM Transactions on Computational Biology and Bioinformatics 18 489-499 (2021)
Ebola Virus VP35 protein: modeling of the tetrameric structure and an analysis of its interaction with Human PKR by Banerjee A., Mitra P. Journal of Proteome Research 19 4533-4542 (2020)
Boosting phosphorylation site prediction with sequence feature-based Machine learning by Maiti S., Hassan A. , Mitra P. PROTEINS: Structure, Function, and Bioinformatics 88 284-291 (2020)
Estimating Change in Foldability due to Multi-point Deletions in Protein Structures by Banerjee A., Kumar A. , Ghosh K. K., Mitra P. Journal of Chemical Information and Modeling 60 6679-6690 (2020)
Estimating the Effect of Single Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein by Banerjee A., Mitra P. Journal of Chemical Information and Modeling 60 3315-3323 (2020)
ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors by Biswas A., Rajesh Y. , Mitra P. , Mandal M. Biochimica et Biophysica Acta - Reviews on Cancer 1874 188389- (2020)
Changing the Apoptosis Pathway through Evolutionary Protein Design by Shultis D., Mitra P. , Huang X. , Johnson J. , Khattak N. A., Gray F. , Piper C. , Czajka J. , Hansen L. , Wan B. , Chinnaswamy K. , Liu L. , Wang M. , Pan J. , Stuckey J. , Cierpicki T. , Borchers C. H., Wang S. , Lei M. , Zhang Y. Journal of Molecular Biology 431 825-841 (2019)
Analyzing change in protein stability associated with Single Point Deletions in a newly defined protein structure database by Banerjee A., Levy Y. , Mitra P. Journal of Proteome Research 18 1402-1410 (2019)
A Network-based Zoning for Parallel Whole-Cell Simulation by Das B., Patil A. R., Mitra P. Bioinformatics 35 88-94 (2019)
Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management by Rajesh Y., Banerjee A. , Pal I. , Biswas A. , Das S. , Dey K. K., Kapoor N. , Ghosh A. K., Mitra P. , Mandal M. Biochimica et Biophysica Acta - General Subjects 1863 1196-1209 (2019)
Ebolavirus interferon antagonists - protein interaction perspectives to combat pathogenesis by Banerjee A., Pal A. , Pal D. , Mitra P. Briefings in Functional Genomics 17(6) 392-401 (2018)
Bacterial flagellar switching: a molecular mechanism directed by the logic of an electric motor by Maiti S., Mitra P. Journal of Molecular Modeling 24 280-289 (2018)
An evolution-based approach to de novo protein design and case study on Mycobacterium Tuberculosis by Mitra P., Shultis D. , Brender J. R., Czajka J. , Marsh D. , Gray F. , Cierpicki T. , Zhang Y. PLoS Computational Biology 9 e1003298- (2013)
EvoDesign: de novo protein design based on structural and evolutionary profiles by Mitra P., Shultis D. , Zhang Y. Nucleic Acids Research 41 W273-W280 (2013)
How many protein-protein interaction types exist in nature? by Garma L., Mukherjee S. , Mitra P. , Zhang Y. PLoS One 7 e389- (2012)
Using correlated parameters for improved ranking of protein-protein docking decoys by Mitra P., Pal D. Journal of Computational Chemistry 32 787-796 (2011)
PRUNE and PROBE two modular web services for protein-protein docking by Mitra P., Pal D. Nucleic Acids Research 39 229-234 (2011)
Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference by Mitra P., Pal D. Structure 19 304-312 (2011)
dockYard - a repository to assist modeling of protein-protein docking by Mitra P., Pal D. Journal of Molecular Modeling 17 599-606 (2011)
Interface of apoptotic protein complexes has distinct properties by Mitra P., Dhar R. , Pal D. In Silico Biology 9 365-378 (2010)
New measures for estimating surface complementarity and packing at protein-protein interfaces by Mitra P., Pal D. FEBS Letters 584 1163-1168 (2010)

Others

DeepPROTECTNeo: A Deep learning-based Personalized and RV-guided Optimization tool for TCR Epitope interaction using Context-aware Transformers by D. D., S. B., A. P., Mitra P. - (2025)
rpcFold: residual parallel convolutional neural network to decipher RNA folding from RNA sequence by Sharma N., Mitra P. - (2025)
E(Q)AGNN-PPIS: Attention Enhanced Equivariant Graph Neural Network for Protein-Protein Interaction Site Prediction by S A., Suvvada R. , Bhowmick P. K., Mitra P. - (2024)
Correction to: ProFuMCell and ProModb: Web services for analyzing interactionâ based functionally localized protein modules in a cell (Journal of Molecular Modeling, (2022), 28, 6, (167), 10.1007/s00894-022-05133-8) by Das B., Mitra P. Journal of Molecular Modeling 29 - (2023)
Deciphering biological evolution exploiting the topology of Protein Locality Graph by Das B., Mitra P. - (2022)
Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India by Sarkar P., Banerjee S. , Saha S. A., Mitra P. , Sarkar S. - (2022)

Book Chapter/Section

Deep Reinforcement Learning in Healthcare and Biomedical Research by Agrawal S., Mitra P. Deep Reinforcement Learning and Its Industrial Use Cases: AI for Real World Applications 179-205 (2024)

Educational Package

Algorithms for protein modelling and engineering by Mitra P. - (2021)

Conferences

Cluster-Based Relative Outlier Under-Sampling Technique by Hassan A., Banerjee R. , Mitra P. , Mitra P. 19th Industrial Conference on Data Mining ICDM 2019 - (2019)
Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis by Maiti S., Mitra P. International Conference on Bioinformatics and Systems Biology (BSB 2018) - (2018)
Computational method to recognize mutation leading to alterations in protein stability and function by Maiti S., Mitra P. IEEE International Conference on Innovative Technologies in Engineering 2018(ICITE OU) - (2018)
Integrin 1 regulates doxorubicin resistance in breast cancer via FAK-mediated activation of ERK1 pathway by Das S., Jena B. C., Mundre S. , Parekh A. , Rajesh Y. , Mitra P. , Mandal M. AACR Annual Meeting 2018 4022-4022 (2018)
An evolution-based approach to de novo protein design and remodeling of protein interactions in Mycobacterium tuberculosis genome by Mitra P., Shultis D. , Zhang Y. Modeling of Protein Interactions - (2012)
Protein-protein docking: simpler approaches for improved prediction by Mitra P., Pal D. International Conference on Mathematical Biology - (2011)
Efficiently screening monomers of proteins using Naive Bayes classifier by Mitra P., Pal D. Asia Pacific Bioinformatics Conference (APBC 2010) 74- (2010)
Protein-Protein Interaction in Apoptosis Process by Dhar R., Mitra P. , Pal D. International Conference on Bioinformatics (InCoB 2006) 287- (2006)
A Two- and Three- Layer Dogleg Channel Routing Algorithm for Minimizing Total Wire Length by Ghoshal N., Mitra P. , Pal R. K. International Conference on Computers and Devices for Communications CNA_0435- (2004)
A Graph Theoretic Approach to Minimize Total Wire Length in Channel Routing by Mitra P., Ghoshal N. , Pal R. K. IEEE TENCON 2003 414-418 (2003)
TAH based Total Wire Length Minimization in Two-Layer Channel Routing by Mitra P., Ghoshal N. , Chatterji A. , Pal R. K. National Conference on Emerging Trends in VLSI Design and Testing (NCVDAT-03) 428-437 (2003)
Total Wire Length Minimization in Channel Routing by Mitra P., Ghoshal N. , Pal R. K. Conference on Horizons of Telecommunication (HOT 2003) 60- (2003)

Symposium

Computational exploration of critical residues aiding in phosphate sink mechanism related to bacterial chemotaxis by Maiti S., Mitra P. IBSE International Symposium "From Genotype to Phenotype: Computational Approaches to Understand Biological Systems" - (2018)
Identifying the nature of the interface in protein-protein complexes by Mitra P. International Symposium on Biocomputing 13- (2010)