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Subhadarshini, S and Tandon, H and Srinivasan, N and Sowdhamini, R (2024) Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation. In: ACS Omega .
Prabantu, VM and Gadiyaram, V and Vishveshwara, S and Srinivasan, N (2023) Comparison of structural networks across homologous proteins. In: Proteins: Structure, Function and Bioinformatics .
Parvathy, J and Yazhini, A and Srinivasan, N and Sowdhamini, R (2023) Interfacial residues in protein�protein complexes are in the eyes of the beholder. In: Proteins: Structure, Function and Bioinformatics .
Bheemireddy, S and Sandhya, S and Srinivasan, N and Sowdhamini, R (2022) Computational tools to study RNA-protein complexes. In: Frontiers in Molecular Biosciences, 9 .
Naveenkumar, N and Prabantu, VM and Vishwanath, S and Sowdhamini, R and Srinivasan, N (2022) Structures of distantly related interacting protein homologs are less divergent than non-interacting homologs. In: FEBS Open Bio .
Paul, A and Subhadarshini, S and Srinivasan, N (2022) Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles. In: Proteins: Structure, Function and Bioinformatics, 90 (3). pp. 747-764.
Ravikumar, A and Gopnarayan, MN and Subramaniam, S and Srinivasan, N (2022) Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography. In: IUCrJ, 9 . pp. 98-103.
Kalmankar, NV and Pavalam, M and Indrakumar, S and Srinivasan, N and Sowdhamini, R (2022) DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. In: Database : the journal of biological databases and curation, 2022 .
Manikandan, P and Sandhya, S and Nadig, K and Paul, S and Srinivasan, N and Rothweiler, U and Singh, M (2022) Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli. In: Nucleic acids research, 50 (3). pp. 1687-1700.
Yazhini, A and Srinivasan, N and Sandhya, S (2022) Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. In: Frontiers in Genetics, 12 .
Narwani, TJ and Srinivasan, N and Chakraborti, S (2021) NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing. In: Scientific Reports, 11 (1).
Yazhini, A and Srinivasan, N and Sandhya, S (2021) Signatures of conserved and unique molecular features in Afrotheria. In: Scientific Reports, 11 (1).
Bheemireddy, S and Sandhya, S and Srinivasan, N (2021) Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins. In: Frontiers in Molecular Biosciences, 8 .
Chakraborti, S and Hatti, K and Srinivasan, N (2021) �All That Glitters Is Not Gold�: High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses. In: International Journal of Molecular Sciences, 22 (13).
Craveur, P and Narwani, TJ and Srinivasan, N and Gelly, J-C and Rebehmed, J and De Brevern, AG (2021) Shaking the β-Bulges. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 (1). pp. 14-18.
Chakraborti, S and Chakraborty, M and Bose, A and Srinivasan, N and Visweswariah, SS (2021) Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation. In: Frontiers in Molecular Biosciences, 8 .
Tandon, H and de Brevern, AG and Srinivasan, N (2021) Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. In: Structure, 29 (4). 371-384.e3.
Ravikumar, A and De Brevern, AG and Srinivasan, N (2021) Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. In: Journal of Physical Chemistry B .
Prabantu, VM and Naveenkumar, N and Srinivasan, N (2021) Influence of Disease-Causing Mutations on Protein Structural Networks. In: Frontiers in Molecular Biosciences, 7 .
Khan, D and Ara, T and Ravi, V and Rajagopal, R and Tandon, H and Parvathy, J and Gonzalez, EA and Asirvatham-Jeyaraj, N and Krishna, S and Mishra, S and Raghu, S and Bhati, AS and Tamta, AK and Dasgupta, S and Kolthur-Seetharam, U and Etchegaray, J-P and Mostoslavsky, R and Rao, PSM and Srinivasan, N and Sundaresan, NR (2021) SIRT6 transcriptionally regulates fatty acid transport by suppressing PPARγ. In: Cell Reports, 35 (9).
Ravikumar, A and Srinivasan, N (2021) Hypervariability of accessible and inaccessible conformational space of proteins. In: Current Research in Structural Biology, 3 . pp. 229-238.
Yazhini, A and Sandhya, S and Srinivasan, N (2021) Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. In: Current Research in Structural Biology, 3 . pp. 133-145.
Janaki, C and Gowri, VS and Srinivasan, N (2021) Master Blaster: an approach to sensitive identification of remotely related proteins. In: Scientific Reports, 11 (1).
Maitra, A and Sarkar, MC and Raheja, H and Biswas, NK and Chakraborti, S and Singh, AK and Ghosh, S and Sarkar, S and Patra, S and Mondal, RK and Ghosh, T and Chatterjee, A and Banu, H and Majumdar, A and Chinnaswamy, S and Srinivasan, N and Dutta, S and Das, S (2020) Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. In: Journal of Biosciences, 45 (1).
Chakraborti, S and Bheemireddy, S and Srinivasan, N (2020) Repurposing drugs against the main protease of SARS-CoV-2: Mechanism-based insights supported by available laboratory and clinical data. In: Molecular Omics, 16 (5). pp. 474-491.
Yazhini, A and Srinivasan, N (2020) How good are comparative models in the understanding of protein dynamics? In: Proteins: Structure, Function and Bioinformatics, 88 (7). pp. 874-888.
Uma Reddy, B and Tandon, H and Pradhan, MK and Adhikesavan, H and Srinivasan, N and Das, S and Jayaraman, N (2020) Potent HCV NS3 Protease Inhibition by a Water-Soluble Phyllanthin Congener. In: ACS Omega, 5 (20). pp. 11553-11562.
Aghera, NK and Prabha, J and Tandon, H and Chattopadhyay, G and Vishwanath, S and Srinivasan, N and Varadarajan, R (2020) Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase. In: Structure, 28 (5). 562-572.e4.
Kumar, G and Srinivasan, N and Sandhya, S (2020) Artificial protein sequences enable recognition of vicinal and distant protein functional relationships. In: Proteins: Structure, Function and Bioinformatics .
Paul, A and Srinivasan, N (2020) Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights. In: Proteins: Structure, Function and Bioinformatics .
Faure, G and Joseph, AP and Craveur, P and Narwani, TJ and Srinivasan, N and Gelly, J-C and Rebehmed, J and De Brevern, AG (2019) IPBAvizu: A PyMOL plugin for an efficient 3D protein structure superimposition approach. In: Source Code for Biology and Medicine, 14 (1).
Kalaivani, R and Narwani, TJ and de Brevern, AG and Srinivasan, N (2019) Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. In: PROTEIN SCIENCE, 28 (3). pp. 543-560.
Balamurugan, K and Bjorkhaug, L and Mahajan, S and Kanthimathi, S and Njolstad, PR and Srinivasan, N and Mohan, V and Radha, V (2016) Structure-function studies of HNF1A (MODY3) gene mutations in South Indian patients with monogenic diabetes. In: CLINICAL GENETICS, 90 (6). pp. 486-495.
Srinivasan, N and Mudgal, R and Kumar, G and Chandra, NR and Sowdhamini, R and Sandhya, S (2015) Bridging the islands of protein families in sequence space using artificial sequences. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). pp. 103-104.
Lakshmi, B and Ramakrishnan, C and Archunan, G and Sowdhamini, R and Srinivasan, N (2014) Investigations of Ramachandran disallowed conformations in protein domain families. In: INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 63 . pp. 119-125.
Rakshambikai, R and Srinivasan, N and Gadkari, Rupali A (2014) REPERTOIRE OF PROTEIN KINASES ENCODED IN THE GENOME OF ZEBRAFISH SHOWS REMARKABLY LARGE POPULATION OF PIM KINASES. In: JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 12 (1).
Sen, Dwaipayan and Gadkari, Rupali A and Sudha, Govindarajan and Gabriel, Nishanth and Ramya, V and Nair, Sukesh C and Srinivasan, N and Srivastava, Alok and Jayandharan, Giridhara R (2013) A novel adeno-associated virus serotype (AAV)-8 capsid mutant improves human coagulation factor IX expression in vivo. In: Molecular Therapy, 21 (1). S47-S47.
Ray, Upasana and Roy, Chaitrali L and Kumar, Anuj and Mani, Prashant and Joseph, Agnel P and Sudha, G and Sarkar, Debi P and Srinivasan, N and Das, Saumitra (2013) Inhibition of the Interaction Between NS3 Protease and HCV IRES With a Small Peptide: A Novel Therapeutic Strategy. In: MOLECULAR THERAPY, 21 (1). pp. 57-67.
Sen, Dwaipayan and Kalaivani, V and Gadkari, Rupali and Sudha, G and Srinivasan, N and Srivastava, Alok and Jayandharan, Giridhara R (2013) Multiple molecular alterations in phosphodegrons 1-3 within AAV2 capsid demonstrates higher hepatic gene transfer efficiency. In: Molecular Therapy, 21 (1). S206-S207.
Lakshmi, B and Archunan, G and Srinivasan, N (2013) PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 128-135.
Gabriel, Nishanth and Duraiswamy, Ramya and Gadkari, Rupali A and Govindarajan, Sudha and Ramakrishna, Banumathi and Srivastava, Arun and Srinivasan, N and Srivastava, Alok and Jayandharan, Giridhara Rao (2012) Targeted Mutagenesis of Ubiquitin-Binding Lysine Residues on the Adeno-Associated Virus (AAV)2 Capsid Improves Its Transduction Efficiency. In: Molecular Therapy, 20 (1). p. 146.
Chawla, Bhavna and Kumar, Ravi Ranjan and Tyagi, Nidhi and Subramanian, Gowri and Srinivasan, N and Park, Myung Hee and Madhubala, Rentala (2012) A Unique Modification of the Eukaryotic Initiation Factor 5A Shows the Presence of the Complete Hypusine Pathway in Leishmania donovani. In: PLos One, 7 (3).
Sandhya, S and Mudgal, R and Jayadev, C and Abhinandan, KR and Sowdhamini, R and Srinivasan, N (2012) Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. In: MOLECULAR BIOSYSTEMS, 8 (8). pp. 2076-2084.
