Anupam Banerjee, Kuntal Pal, Pralay Mitra (In press). 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
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
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
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
David Shultis, Pralay Mitra, ... , 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
Barnali Das, Abhijeet Rajendra Patil, Pralay Mitra (2019). A Network-based Zoning for Parallel Whole-Cell Simulation.
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
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
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
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
Leonardo Garma, Srayanta Mukherjee, Pralay Mitra, Yang Zhang (2012). How many protein-protein
interaction types exist in nature? PLoS ONE 7(6): e38913.
Pralay Mitra, Debnath Pal (2011). PRUNE and PROBE - two modular web services for protein-protein docking.
Nucleic Acids Research 39(W):229-234.
[PubMed] Listed as OMIC-tools under Drug Discovery|
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.
Among Top 10 Most Read Articles at Structure until April 2011. |
Pralay Mitra, Debnath Pal (2011). Using correlated parameters for improved ranking of protein-protein
docking decoys. Journal of Computational Chemistry 32(5):787-796.
Pralay Mitra, Debnath Pal (2011). dockYard - a repository to assist modeling of protein-protein docking.
Journal of Molecular Modeling 17(3):599-606.
Pralay Mitra, Debnath Pal (2010). New measures for estimating surface complementarity and packing at
protein-protein interfaces. FEBS Letters 584(6):1163-1168.
|1.||Pralay Mitra, Riddhiman Dhar, Debnath Pal (2010). Interface of apoptotic protein complexes has distinct properties. In Silico Biology 9(5-6):365-378. [PubMed]|
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. ||12.||
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. ||11.||
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.
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||9.||
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. ||8.||
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. ||7.||
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] ||6.||
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. ||5.||
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.||4.||
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. ||3.||
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.
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.||1.||
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
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). 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.
|1.||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.|
Pralay Mitra (2010). Algorithmic Approaches for Protein-Protein Docking and Quaternary Structure Inference.
Indian Institute of Science, Bangalore
Thesis Advisor: Debnath Pal
Pralay Mitra (2004). Map Assembly Problem. Bengal Enginerring and Science University, Shibpur.
Thesis Advisor: Alak Kumar Datta
Pralay Mitra, Arijit Chatterji (2002). High Performance Two Layer Channel Routing.
University of Calcutta
Thesis Advisor: Rajat Kumar Pal