Welcome to CoSMoS

Computations in Structural, Molecular, and Systems biology

Publications

                   

Book Chapter

• Pralay Mitra, Soumyadeep Bhaduri, Debraj Das, Dibya Kanti Haldar (2026). Artificial intelligence-assisted drug designing, toxicity assessment, and biodelivery. Applications of Artificial Intelligence in Healthcare: The Changing Landscape 417-433    [DOI]    [Link]

• Shruti Agrawal, Pralay Mitra (2024). Deep Reinforcement Learning in Healthcare and Biomedical Research. Deep Reinforcement Learning and Its Industrial Use Cases: AI for Real‐World Applications 179-205    [DOI]    [SCOPUS]
  

Journal Papers

• Debraj Das, Soumyadeep Bhaduri, Pralay Mitra (2026). DeepPROTECTNeo: a context-aware personalised and reverse vaccinology-guided deep learning framework for immunogenicity prediction. BMC Biology 27 pages    [PubMed]    [SpringerLink]     IF:5.7
  
  
• Suvendu Nandi, Shreya Banerjee, Debolina Manna, Animesh Awasthi, Angana Biswas, Abhijit Das, Budhaditya Mukherjee, Pralay Mitra, Mahitosh Mandal (2026). Targeting of HSP27 and MMP-2 /9 Crosstalk by High Throughput Drug Repurposing Strategies Identifies Paroxetine as a Potential Candidate in Glioblastoma. Journal of Medicinal Chemistry 69(4):4659-4676    [PubMed]    [DOI]     IF:6.8
  
  
• Dibya Kanti Haldar, Avik Pramanick, Chandrama Mukherjee, Pralay Mitra (2026). A transformer based method for the Cap analysis of gene expression and gene expression tag associated capping region prediction in RNA. RNA Biology 23(1):1-15    [PubMed]    [DOI]     IF:3.9
  
  
• Shubhrangshu Ghosh, Pralay Mitra (2026). PEPpip: A Vision-Inspired Explainable Deep Learning Framework for Sequence-Based Protein-Protein Interaction Prediction and Interaction Map Estimation. IEEE Access 14:16936-16949    [IEEE]    [DOI]     IF:3.6
  
  
• Shruti Agrawal, Pralay Mitra (2026). From Molecular Heterogeneity to Clinical Precision: Multi-Omics Machine Learning for Personalized Risk Stratification in Lung Adenocarcinoma. In Silico Research in Biomedicine    [DOI]   
  
  
• Somarpita Dutta, Pralay Mitra (2026). Deep learning framework reveals drug combinations involving Dipeptidyl peptidase-4 inhibitors for treatment of Polycystic Ovarian Syndrome on a heterogeneous network. In Silico Research in Biomedicine 2:100223 (14 pages)    [DOI]   
  
  
• Animesh, Rishi Suvvada, Plaban Kumar Bhowmick, Pralay Mitra (2025). E(Q)AGNN-PPIS: Attention Enhanced Equivariant Graph Neural Network for Protein-Protein Interaction Site Prediction. IEEE Transactions on Signal and Information Processing over Networks 11:740-751    [IEEE]    [DOI]     IF:4.9
  
  
• Siddik Sarkar, Sarbar Ali Saha, Abhishek Swarnakar, Arnab Chakrabarty, Avipsa Dey, Poulomi Sarkar, Sarthak Banerjee, Pralay Mitra (2024). The molecular prognostic score, a classifier for risk stratification of high-grade serous ovarian cancer. Journal of Ovarian Research 17(1):159 (14 pages)    [PubMed]    [DOI]     IF:3.8
  
  
• Suvendu Nandi, Soumyadeep Bhaduri, Debraj Das, Priya Ghosh, Mahitosh Mandal, Pralay Mitra (2024). Deciphering the Lexicon of Protein Targets: A review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. ACS Molecular Pharmaceutics 21(4):1563–1590    [PubMed]    [DOI]     IF:4.9
  
  
• Shubhrangshu Ghosh, Pralay Mitra (2024). MaTPIP: a deep-learning architecture with eXplainable AI for sequence-driven, feature mixed protein-protein interaction prediction. Computer Methods and Programs in Biomedicine 244:107955 (12 pages)    [PubMed]        [DOI]     IF:6.1
  
  
• Subhayan Das, Moumita Kundu, Atif Hassan, Aditya Parekh, Bikash Ch Jena, Swati Mundre, Indranil Banerjee, Rajesh Yeitrajam, Chandan K Das, Anjan K Pradhan, Swadesh K Das, Luni Emdad, Pralay Mitra, Paul B Fisher, Mahitosh Mandal (2023). A novel computational predictive biological approach distinguishes Integrin β1 as a salient biomarker for breast cancer chemoresistance. Biochimica et Biophysica Acta - Molecular Basis of Disease (BBADIS) 1869(6):166702 (17 pages)    [PubMed]    [DOI]    IF:6.633
  
  
• Poulomi Sarkar, Sarthak Banerjee, Sarbar Ali Saha, Pralay Mitra, Siddik Sarkar (2023). Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. Scientific Reports 13(1) Article number: 4692 (10 pages)    [PubMed]     [DOI]     IF:4.996
  
  
• Ayush Malik, Anupam Banerjee, Abantika Pal, Pralay Mitra (2023). A sequence space search engine for computational protein design to modulate molecular functionality. Journal of Biomolecular Structure & Dynamics 41(7):2937-2946    [PubMed]     IF:3.549
  
  
• Angana Biswas, Yetirajam Rajesh, Subhayan Das, Indranil Banerjee, Neelkamal Kapoor, Pralay Mitra, Mahitosh Mandal (2022). Therapeutic targeting of RBPJ, an upstream regulator of ETV6 gene, abrogates ETV6-NTRK3 fusion gene transformations in glioblastoma. Cancer Letters 544:215811 (14 pages)    [PubMed]     [DOI]     IF:9.756
  
  
• Puspita Halder, Pralay Mitra (2022). Human Prion Protein: Exploring the Thermodynamic Stability and Structural Dynamics of its Pathogenic Mutants. Journal of Biomolecular Structure & Dynamics 40(21):11274-11290    [PubMed]     IF:3.549
  
  
• Barnali Das, Pralay Mitra (2022). ProFuMCell and ProModb: web services for analyzing interaction-based functionally localized protein modules in a cell. Journal of Molecular Modeling 28(6):167 (8 pages)    [PubMed]     IF:1.871
  
  
• Abantika Pal, Rohith Mulumudy, Pralay Mitra (2022). Modularity-based Parallel Protein Design Algorithm with an Implementation using Shared Memory Programming. PROTEINS: Structure, Function, and Bioinformatics 90(3):658-669    [PubMed]     IF:3.756
  
  
• Barnali Das, Pralay Mitra (2021). Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins. Journal of Molecular Biology 433(19):167149    [PubMed]     IF:5.469
  
  
• Abantika Pal, Debnath Pal, Pralay Mitra (2021). A computational framework for modeling functional protein-protein interactions. PROTEINS: Structure, Function, and Bioinformatics 89(10):1353-1364    [PubMed]     IF:3.756
  
  
• Barnali Das, Pralay Mitra (2021). High-performance Whole-cell Simulation Exploiting Modular Cell Biology Principles. Journal of Chemical Information and Modeling 61(3):1481-1492    [PubMed]     IF:4.956
  
  
• Anupam Banerjee, Kuntal Pal, Pralay Mitra (2021). An evolutionary profile guided greedy parallel replica-exchange Monte Carlo search algorithm for rapid convergence in protein design. IEEE/ACM Transactions on Computational Biology and Bioinformatics 18(2):489-499    [PubMed]     IF:3.015
  
  
• Anupam Banerjee, Amit Kumar, Kushal Kanti Ghosh, Pralay Mitra (2020). Estimating Change in Foldability due to Multi-point Deletions in Protein Structures. Journal of Chemical Information and Modeling 60(12):6679-6690    [PubMed]     IF:4.956
  
  
• Anupam Banerjee, Pralay Mitra (2020). Ebola Virus VP35 protein: modeling of the tetrameric structure and an analysis of its interaction with Human PKR. Journal of Proteome Research 19(11):4533-4542    [PubMed]     Free PMC article     IF:4.466     The article is part of the Proteomics in Pandemic Disease special issue.
  
  
• Angana Biswas, Yetirajam Rajesh, Pralay Mitra, Mahitosh Mandal (2020). ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors. Biochimica et Biophysica Acta - Reviews on Cancer 1874(1):188389 (12 pages)    [PubMed]     IF:7.365
  
  
• Anupam Banerjee, Pralay Mitra (2020). Estimating the Effect of Single Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein. Journal of Chemical Information and Modeling 60(6):3315-3323    [PubMed]     IF:4.956
  
  
• Shyantani Maiti, Atif Hassan, Pralay Mitra (2020). Boosting phosphorylation site prediction with sequence feature-based Machine learning. PROTEINS: Structure, Function, and Bioinformatics 88(2):284-291    [PubMed]     IF:3.756
  
  
• Rajesh Y, Anupam Banerjee, Ipsita Pal, Angana Biswas, Subhayan Das, Kaushik K Dey, Neelkamal Kapoor, Ananta K Ghosh, Pralay Mitra, Mahitosh Mandal (2019). Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management. Biochimica et Biophysica Acta - General Subjects 1863(7):1196-1209    [PubMed]     IF:3.679
  
  
• Anupam Banerjee, Yaakov Levy, Pralay Mitra (2019). Analyzing change in protein stability associated with Single Point Deletions in a newly defined protein structure database. Journal of Proteome Research 18(3):1402-1410    [PubMed]     IF:4.466
  
  
• David Shultis, Pralay Mitra, Xiaoqiang Huang, Jarrett Johnson, Naureen Aslam Khattak, Felicia Gray, Clint Piper, Jeff Czajka, Logan Hansen, Bingbing Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, Jeanne Stuckey, Tomasz Cierpicki, Christoph H Borchers, Shaomeng Wang, Ming Lei, Yang Zhang (2019). Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology 431(4):825-841    [PubMed]     Free PMC article     IF:4.894
  
  
• Barnali Das, Abhijeet Rajendra Patil, Pralay Mitra (2019). A Network-based Zoning for Parallel Whole-Cell Simulation. Bioinformatics 35(1):88-94    [PubMed]     IF:5.481
  
  
• Shyantani Maiti, Pralay Mitra (2018). Bacterial flagellar switching: a molecular mechanism directed by the logic of an electric motor. Journal of Molecular Modeling 24:280    [PubMed]     IF:1.871
  
  
• Anupam Banerjee, Abantika Pal, Debnath Pal, Pralay Mitra (2018). Ebolavirus interferon antagonists-protein interaction perspectives to combat pathogenesis. Briefings in Functional Genomics 17(6):392-401    [PubMed]     IF:4.098
  
  
• Pralay Mitra, David Shultis, Jeffrey R Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang (2013). An evolution-based approach to de novo protein design and case study on Mycobacterium Tuberculosis. PLoS Computational Biology 9(10): e1003298    [PubMed]     Free PMC article     IF:5.939
  
  
• Pralay Mitra, David Shultis, Yang Zhang (2013). EvoDesign: de novo protein design based on structural and evolutionary profiles. Nucleic Acids Research 41(W):273-280    [PubMed]     Free PMC article         IF:8.278
  
  
• Leonardo Garma, Srayanta Mukherjee, Pralay Mitra, Yang Zhang (2012). How many protein-protein interaction types exist in nature? PLoS ONE 7(6):e38913.    [PubMed]     Free PMC article     IF:4.537
  
  
• Pralay Mitra, Debnath Pal (2011). PRUNE and PROBE - two modular web services for protein-protein docking. Nucleic Acids Research 39(W):229-234.    [PubMed]     Free PMC article     Listed as OMIC-tools under Drug Discovery     IF:8.278
  
  
• Pralay Mitra, Debnath Pal (2011). Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference. Structure 19(3):304-312.    [PubMed]    Among Top 10 Most Read Articles at Structure until April 2011.     IF:6.347
  
  
• Pralay Mitra, Debnath Pal (2011). Using correlated parameters for improved ranking of protein-protein docking decoys. Journal of Computational Chemistry 32(5):787-796.    [PubMed]     IF:4.583
  
  
• Pralay Mitra, Debnath Pal (2011). dockYard - a repository to assist modeling of protein-protein docking. Journal of Molecular Modeling 17(3):599-606.    [PubMed]     IF:1.871
  
  
• Pralay Mitra, Debnath Pal (2010). New measures for estimating surface complementarity and packing at protein-protein interfaces. FEBS Letters 584(6):1163-1168.    [PubMed]     IF:3.601
  
  
• Pralay Mitra, Riddhiman Dhar, Debnath Pal (2010). Interface of apoptotic protein complexes has distinct properties. In Silico Biology 9(5-6):365-378.    [PubMed]

Conference Papers and Presentations

• Purnima Gautam, Pralay Mitra (in press). EpiESM-GA: Resource-Efficient Protein Foundation Model Features for Equitable B-Cell Epitope Prediction. In Proc. of Workshop on Foundation Models for Social Good: Co-located with IJCAI-ECAI 2026, Bremen, Germany, 2026,   
  
  
• Purnima Gautam, Pralay Mitra (2026). HALPred-B: Host-Aware Linear B-Cell Epitope Prediction: Challenges, Limitations, and Variability Across Species. In Proc. of IEEE 50th Annual Computers, Software, and Applications Conference (COMPSAC), Madrid, Spain, 2026, pp. 2161-2166    [DOI]
  
  
• Shruti Agrawal, Pralay Mitra (2026). Engineered miRNA Feature–Driven Machine Learning Models for Risk Stratification in Lung Adenocarcinoma. In Proc. of IEEE 50th Annual Computers, Software, and Applications Conference (COMPSAC), Madrid, Spain, 2026, pp. 793-798    [DOI]
  
  
• Nandita Sharma, Pralay Mitra (2026). A Sequence Feature-based Deep Learning Framework for Automatic Family Classification of the Small Non-Coding RNA. In Proc. of IEEE 50th Annual Computers, Software, and Applications Conference (COMPSAC), Madrid, Spain, 2026, pp. 3022-3027    [DOI]
  
  
• Shubhrangshu Ghosh, Pralay Mitra (2026). An Artificial Intelligence-based framework for protein interaction design with accelerated KAN-based Positive-Unlabeled learning. In Proc. of International Conference on Advanced Scientific Computing & Machine Learning (ASCML 2026), BITS Pilani, Goa, India, February 10-12, 2026.    [Link]
  
  
• Shruti Agrawal, Pralay Mitra (2026). Identification of a Novel miRNA Expression Signature for Lung Adenocarcinoma Using Systematic Machine Learning Optimization. In Proc. of International Conference on Advanced Scientific Computing & Machine Learning (ASCML 2026), BITS Pilani, Goa, India, February 10-12, 2026.
  
  
• Purnima Gautam, Pralay Mitra (2025). ConfPred: ML-Based Conformational B-cell Epitope Prediction Using Novel Features. 12th International Conference on Bioinformatics Research and Applications(ICBRA 2025), Prague, Czech Republic, September 19-21, 2025. ACM Digital Library
  
  
• Shruti Agrawal, Pralay Mitra (2025). AI-Driven Computational Protein Design for Cancer Drug Discovery Using Deep Reinforcement Learning. Accepted for poster presentation at the 29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025), Seoul, Korea, April 26-29, 2025.
  
  
• Nandita Sharma, Pralay Mitra (2025). A residual parallel convolutional neural network designed to unravel RNA folding patterns directly from RNA sequences. Accepted for poster presentation at the 29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025), Seoul, Korea, April 26-29, 2025.
  
  
• Atif Hassan, Rohini Banerjee, Pabitra Mitra, Pralay Mitra (2019). Cluster-Based Relative Outlier Under-Sampling Technique. In Proc. of 19th Industrial Conference on Data Mining ICDM 2019 (ICDM 2019), New York, USA, July 17-21, 2019.
  
  
• Subhayan Das, Bikash Ch Jena, Swati Mundre, Aditya Parekh, Y Rajesh, Pralay Mitra, Mahitosh Mandal (2018). Integrin β1 regulates doxorubicin resistance in breast cancer via FAK-mediated activation of ERK1 pathway. Cancer Research 78(13 Supplement):4022-4022. In Proc. of AACR Annual Meeting 2018, Chicago, IL, USA, April 14-18, 2018.
  
  
• Shyantani Maiti, Pralay Mitra (2018). Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis. In Proc. of 2018 International Conference on Bioinformatics and Systems Biology (BSB-2018), pp. 32-35, Allahabad, India, Oct 26-28, 2018.    [IEEE Xplore]
  
  
• Shyantani Maiti, Pralay Mitra (2018). Computational method to recognize mutation leading to alterations in protein stability and function. In Proc. of IEEE International Conference on Innovative Technologies in Engineering 2018 (ICITE OU), Hyderabad, India, Apr 11-13, 2018.    Awarded as Best Paper in Computer Science and Engineering
  
  
• Pralay Mitra, David Shultis, Yang Zhang (2012). An evolution-based approach to de novo protein design and remodeling of protein interactions in Mycobacterium tuberculosis genome. Presented at Modeling of Protein Interactions (MPI 2012), Lawrence, Kansas, USA, Nov 08-10, 2012.
  
  
• Pralay Mitra, Debnath Pal (2011). Protein-protein docking: simpler approaches for improved prediction. Presented at the International Conference on Mathematical Biology, Bangalore, India, Jul 04-07, 2011.
  
  
• Pralay Mitra (2010). Identifying the nature of the interface in protein-protein complexes. In Proc. of International Symposium on Biocomputing (ISB 2010), Article No: 13, ACM Digital Library, Calicut, India, Feb 15-17, 2010.    [ACM Portal]
  
  
• Pralay Mitra, Debnath Pal (2010). Efficiently screening monomers of proteins using Naive Bayes classifier. Presented at the Eighth Asia Pacific Bioinformatics Conference (APBC 2010), Poster ID: 74, Bangalore, India, Jan 18-21, 2010.
  
  
• Riddhiman Dhar, Pralay Mitra, Debnath Pal (2006). Protein-Protein Interaction in Apoptosis Process. In Proc. of International Conference on Bioinformatics (InCoB 2006), Paper ID: P287, New Delhi, India, Dec 18-20, 2006.
  
  
• Nabin Ghoshal, Pralay Mitra, Rajat K. Pal (2004). A Two- and Three- Layer Dogleg Channel Routing Algorithm for Minimizing Total Wire Length. In Proc. of International Conference on Computers and Devices for Communications (CODEC-04), Paper ID: CNA_0435_CO, Kolkata, India, Jan 1-3, 2004.
  
  
• Pralay Mitra, Nabin Ghoshal, Rajat K. Pal (2003). A Graph Theoretic Approach to Minimize Total Wire Length in Channel Routing. In Proc. of 18th IEEE Region 10 International Conf on Computers, Communications, Control and Power Engineering (IEEE TENCON 2003), Vol. 1, pp 414-418, Bangalore, India, Oct 15-17, 2003.    [IEEE Xplore]
  
  
• Pralay Mitra, Nabin Ghoshal, Arijit Chatterji, Rajat K. Pal (2003). TAH based Total Wire Length Minimization in Two-Layer Channel Routing. In Proc. of National Conference on Emerging Trends in VLSI Design and Testing (NCVDAT-03), pp 428-437, Coimbatore, India, Feb 21-22, 2003.
  
  
• Pralay Mitra, Nabin Ghoshal, Rajat K. Pal (2003). Total Wire Length Minimization in Channel Routing. In Proc. of Conference on Horizons of Telecommunication (HOT 2003), page 60, Kolkata, India, Feb 3-5, 2003