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 articleIF: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 articleIF: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
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 articleIF: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 articleIF: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 articleIF: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
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 Research78(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
Archived Papers
Siddik Sarkar, Sarbar Ali Saha, Poulomi Sarkar, Sarthak Banerjee, Pralay Mitra (2023). The molecular prognostic score, a classifier for risk stratification of high-grade serous ovarian cancer. In bioRxiv, [DOI]
Poulomi Sarkar, Sarthak Banerjee, Sarbar Ali Saha, Pralay Mitra, Siddik Sarkar (2022). Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. In medRxiv, [DOI]
Barnali Das, Pralay Mitra (2021). Deciphering biological evolution exploiting the topology of Protein Locality Graph. In bioRxiv, 446976 [DOI]
Gazal Kalyan, Vivek Junghare, Anupam Chattopadhyay, Pralay Mitra, Saugata Hazra (2019). Parsers, data structures and algorithms for Macromolecular Analysis Toolkit (MAT): Design and implementation. In bioRxiv, 605907 [DOI]
Pralay Mitra (2024). Organized Two-Day Hands-on Workshop on High-Performance Computing in Bioinformatics under National Supercomputing Mission, Center for Computational Data Sciences, Indian Institute of Technology Kharagpur, West Bengal - 721302, India, Feb 10-11, 2024.
Pralay Mitra (2023). MATLAB and its Application. Presented at the Faculty Development programme on "MATLAB and its Applications", Department of Computer Application, Maharaja Sriram Chandra Bhanja Deo University, Baripada - 757003, Orissa, India, May 16-20, 2023.
Pralay Mitra (2023). Artificial Intelligence to Infer Drug-Disease Association from Protein Interaction Network. Presented at the Faculty Development programme on "Advancements in Computational Biology and Healthcare", Department of Electronics and Communication Engineering, SRM University-AP, Andhra Pradesh - 522240, India, April 17-21, 2023.
Pralay Mitra (2021). Application of Machine Learning in Bioinformatics. Presented at the Five-day Faculty Development Program on Artificial Intelligence, Ramakrishna Mission Vivekananda University, Belur Math, India, Feb 01-05, 2021.
Pralay Mitra (2021). Role of Protein Design in Drug Discovery. Presented at the International Webinar on "Impact of Digital Revolution on Pharma & Healthcare", Indian Institute of Engineering Science and Technology (IIEST), West Bengal, India, Jan 29 - Feb 02, 2021.
Pralay Mitra, C. Unnikrishnan (2020). Shared Memory Programming with OpenMP. Delivered lectures at Basics of High Performance Computing under HPC Shiksha, Online Dec 09-30, 2020.
Pralay Mitra (2020). Participated in the panel discussion on Communication Technologies for IoT/Cyber Physical Systems under Communication Technologies vertical at the VAIBHAV summit, Online Oct 13, 2020.
Pralay Mitra (2020). Chaired the panel discussion on High Performance Computing and its Applications under Computational Sciences vertical at the VAIBHAV summit, Online Oct 04, 2020.
Pralay Mitra (2018). Computational protein design and its applications. Presented as departmental colloquium at the Department of Life Sciences, Presidency University, West Bengal India, Aug 29, 2018.
Pralay Mitra (2018). Bioinformatics: Present and Future. Presented at the Big Data Analytics Workshop, Ramakrishna Mission Vivekananda University, Belur Math, India, Feb 24, 2018.
Pralay Mitra (2016). An evolution-based approach to de novo protein design. Presented as departmental seminar at the Department of Structural Biology, Weizmann Institute of Science, Israel, Sept 15, 2016.
Pralay Mitra (2016). Computational Protein Design. Presented at the Workshop on Mathematical and Computational Biology, NNMCB Kolkata Node,
IISER Kolkata, Mohanpur Campus, India, Jan 10, 2016.
Pralay Mitra (2013). Algorithmic Techniques for Modeling. Presented at the Emerging Research Trends in Data Mining For Bioinformatics, AU College of Engineering, Andhra University, India, Dec 20, 2013.
Pralay Mitra (2013). Computational Perspectives of Protein Interactions. Presented at the Indo-Brazil Workshop on Biomedical Informatics, Indian Institute of Technology, Kharagpur, India, Sept 4, 2013.
Ph.D. Dissertation
Pralay Mitra (2010). Algorithmic Approaches for Protein-Protein Docking and Quaternary Structure Inference. Indian Institute of Science, Bangalore Thesis Advisor: Debnath Pal
Contact us:
Department of Computer Science and Engineering
Indian Institute of Technology Kharagpur
Paschim Midnapur, West Bengal - 721302, India
Phone: +91-3222-282344
Email: pralay[at]cse[dot]iitkgp[dot]ac[dot]in
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IF:8.278