|
 | Up a level |
Kumar, Gayatri and Srinivasan, Narayanaswamy and Sandhya, Sankaran (2022) Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. [Book Chapter]
Prabantu, Vasam Manjveekar and Gadiyaram, Vasundhara and Vishveshwara, Saraswathi and Srinivasan, Narayanaswamy (2022) Understanding structural variability in proteins using protein structural networks. In: Current Research in Structural Biology, 4 . pp. 134-145. ISSN 2665928X
Janaki, Chintalapati and Malini, Manoharan and Tyagi, Nidhi and Srinivasan, Narayanaswamy (2020) Unity and diversity among viral kinases. In: GENE, 723 .
Ravikumar, Ashraya and Ramakrishnan, Chandrasekharan and Srinivasan, Narayanaswamy (2019) Stereochemical Assessment of (phi,psi) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps. In: STRUCTURE, 27 (12). 1875+.
Vetrivel, Iyanar and de Brevern, Alexandre G and Cadet, Frederic and Srinivasan, Narayanaswamy and Offmann, Bernard (2019) Structural variations within proteins can be as large as variations observed across their homologues. In: BIOCHIMIE, 167 . pp. 162-170.
Kidwai, Saqib and Bouzeyen, Rania and Chakraborti, Sohini and Khare, Neha and Das, Sumana and Gosain, Tannu Priya and Behura, Assirbad and Meena, Chhuttan Lal and Dhiman, Rohan and Essafi, Makram and Bajaj, Avinash and Saini, Deepak Kumar and Srinivasan, Narayanaswamy and Mahajan, Dinesh and Singh, Ramandeep (2019) NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G. In: ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 63 (9).
Naveenkumar, Nagarajan and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy (2019) Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. In: FEBS OPEN BIO, 9 (11). pp. 1848-1859.
Tandon, Himani and Sharma, Arun and Wadhwa, Saruchi and Varadarajan, Raghavan and Singh, Ramandeep and Srinivasan, Narayanaswamy and Sandhya, Sankaran (2019) Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 294 (23). pp. 9048-9063.
Tandon, Himani and Sharma, Arun and Sandhya, Sankaran and Srinivasan, Narayanaswamy and Singh, Ramandeep (2019) Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. In: SCIENTIFIC REPORTS, 9 .
Tandon, Himani and Sharma, Arun and Sandhya, Sankaran and Srinivasan, Narayanaswamy and Singh, Ramandeep (2019) Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. In: SCIENTIFIC REPORTS, 9 .
Jayashree, Srinivasan and Murugavel, Pavalam and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy (2019) Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions. In: BIOLOGY DIRECT, 14 .
Mehrotra, Prachi and Ami, Vimla Kany G and Srinivasan, Narayanaswamy (2018) Clustering of multi-domain protein sequences. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 86 (7). pp. 759-776.
Kumar, Gayatri and Mudgal, Richa and Srinivasan, Narayanaswamy and Sandhya, Sankaran (2018) Use of designed sequences in protein structure recognition. In: BIOLOGY DIRECT, 13 .
Bhagavat, Raghu and Sankar, Santhosh and Srinivasan, Narayanaswamy and Chandra, Nagasuma (2018) An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure. In: STRUCTURE, 26 (3). 499+.
Vishwanath, Sneha and de Brevern, Alexandre G and Srinivasan, Narayanaswamy (2018) Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. In: PLOS COMPUTATIONAL BIOLOGY, 14 (2).
Reddy, B Uma and Mullick, Ranajoy and Kumar, Anuj and Sharma, Geetika and Bag, Paromita and Roy, Chaitrali Laha and Sudha, Govindarajan and Tandon, Himani and Dave, Pratik and Shukla, Ashutosh and Srinivasan, Priyanka and Nandhitha, Madhusudhan and Srinivasan, Narayanaswamy and Das, Saumitra (2018) A natural small molecule inhibitor corilagin blocks HCV replication and modulates oxidative stress to reduce liver damage. In: ANTIVIRAL RESEARCH, 150 . pp. 47-59.
Bhagavat, Raghu and Kim, Heung-Bok and Kim, Chang-Yub and Terwilliger, Thomas C and Mehta, Dolly and Srinivasan, Narayanaswamy and Chandra, Nagasuma (2017) A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis. In: SCIENTIFIC REPORTS, 7 (1).
Hatti, Kaushik and Mathiharan, Yamuna Kalyani and Srinivasan, Narayanaswamy and Murthy, Mathur RN (2017) Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein fromSalmonella typhimurium. In: Acta Crystallographica Section D Structural Biology, 73 (7). pp. 609-617. ISSN 2059-7983
Mehrotra, Prachi and Ramakrishnan, Gayatri and Dhandapani, Gunasekaran and Srinivasan, Narayanaswamy and Madanan, Madathiparambil G (2017) Comparison of Leptospira interrogans and Leptospira biflexa genomes: analysis of potential leptospiral-host interactions. In: MOLECULAR BIOSYSTEMS, 13 (5). pp. 883-891.
Blagavat, Raghu and Srinivasan, Narayanaswamy and Chandra, Nagasuma (2017) Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 85 (9). pp. 1699-1712.
Vishwanath, Sneha and Banerjee, Sunaina and Jamithireddy, Anil K and Srinivasan, Narayanaswamy and Gopal, Balasubramanian and Chatterjee, Jayanta (2017) Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting Mycobacterium tuberculosis sigma Factors. In: BIOCHEMISTRY, 56 (16). pp. 2209-2218.
Ramakrishnan, Gayatri and Chandra, Nagasuma and Srinivasan, Narayanaswamy (2017) Exploring anti-malarial potential of FDA approved drugs: an in silico approach. In: MALARIA JOURNAL, 16 .
Das, Soma and Mullick, Ranajoy and Kumar, Anuj and Tandon, Himani and Bose, Mihika and Gouthamchandra, K and Chandra, Madhavi and Ravishankar, Bagepally and Khaja, M N and Srinivasan, Narayanaswamy and Das, Saumitra and Subbarao, Shaila Melkote and Karande, Anjali Anoop (2017) Identification of a novel epitope in the C terminus of hepatitis C virus-E2 protein that induces potent and cross-reactive neutralizing antibodies. In: JOURNAL OF GENERAL VIROLOGY, 98 (5). pp. 962-976.
Vetrivel, Iyanar and Mahajan, Swapnil and Tyagi, Manoj and Hoffmann, Lionel and Sanejouand, Yves-Henri and Srinivasan, Narayanaswamy and de Brevern, Alexandre G and Cadet, Frederic and Offmann, Bernard (2017) Knowledge-based prediction of protein backbone conformation using a structural alphabet. In: PLOS ONE, 12 (11).
Rakesh, Ramachandran and Krishnan, Rangachari and Sattlegger, Evelyn and Srinivasan, Narayanaswamy (2017) Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. In: BIOLOGY DIRECT, 12 .
Mudgal, Richa and Srinivasan, Narayanaswamy and Chandra, Nagasuma (2017) Resolving protein structure-function-binding site relationships from a binding site similarity network perspective. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 85 (7). pp. 1319-1335.
Chandra, Sunandini and Kalaivani, Raju and Kumar, Manoj and Srinivasan, Narayanaswamy and Sarkar, Debi P (2017) Sendai virus recruits cellular villin to remodel actin cytoskeleton during fusion with hepatocytes. In: MOLECULAR BIOLOGY OF THE CELL, 28 (26). pp. 3801-3814.
Vishwanath, Sneha and Sukhwal, Anshul and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy (2017) Specificity and stability of transient protein-protein interactions. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 44 . pp. 77-86.
Hatti, Kaushik and Biswas, Ansuman and Chaudhary, Santosh and Dadireddy, Venkatareddy and Sekar, Kanagaraj and Srinivasan, Narayanaswamy and Murthy, Mathur R N (2017) Structure determination of contaminant proteins using the MarathonMR procedure. In: JOURNAL OF STRUCTURAL BIOLOGY, 197 (3). pp. 372-378.
Sudha, Govindarajan and Srinivasan, Narayanaswamy (2016) Comparative analyses of quaternary arrangements in homo-oligomeric proteins in superfamilies: Functional implications. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84 (9). pp. 1190-1202.
Ramakrishnan, Gayatri and Jain, Abha and Chandra, Nagasuma and Srinivasan, Narayanaswamy (2016) Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. In: BIOLOGY DIRECT, 11 .
Kalaivani, Raju and de Brevern, Alexandre G and Srinivasan, Narayanaswamy (2016) Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84 (7). pp. 957-978.
Hatti, Kaushik and Gulati, Ashutosh and Srinivasan, Narayanaswamy and Murthy, MRN (2016) Determination of crystal structures of proteins of unknown identity using a marathon molecular replacement procedure: structure of Stenotrophomonas maltophilia phosphate-binding protein. In: ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 72 (10). pp. 1081-1089.
Das, Mrinmoy and Bhosale, Manoj and Wadhwa, Nitin and Ahmed, Syed M and Bhaskarla, Chetana and Kumar, Anujith and Srinivasan, Narayanaswamy and Nandi, Dipankar (2016) Importance of Amino Acids, Gln-119 and Tyr-376, in the S1 Pocket of Escherichia coli Peptidase N in Determining Substrate Specificity. In: PROTEIN AND PEPTIDE LETTERS, 23 (6). pp. 548-561.
Sandhya, Sankaran and Mudgal, Richa and Kumar, Gayatri and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy (2016) Protein sequence design and its applications. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 37 . pp. 71-80.
Rakesh, Ramachandran and Joseph, Agnel Praveen and Bhaskara, Ramachandra M and Srinivasan, Narayanaswamy (2016) Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. In: RNA BIOLOGY, 13 (10). pp. 1025-1040.
Joseph, Agnel P and Swapna, Lakshmipuram S and Rakesh, Ramachandran and Srinivasan, Narayanaswamy (2016) Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting. In: JOURNAL OF STRUCTURAL BIOLOGY, 195 (3). pp. 294-305.
Babbitt, Patricia C and Bagos, Pantelis G and Bairoch, Amos and Bateman, Alex and Chatonnet, Arnaud and Chen, Mark Jinan and Craik, David J and Finn, Robert D and Gloriam, David and Haft, Daniel H and Henrissat, Bernard and Holliday, Gemma L and Isberg, Vignir and Kaas, Quentin and Landsman, David and Lenfant, Nicolas and Manning, Gerard and Nagano, Nozomi and Srinivasan, Narayanaswamy and O'Donovan, Claire and Pruitt, Kim D and Sowdhamini, Ramanathan and Rawlings, Neil D and Saier, Milton H and Sharman, Joanna L and Spedding, Michael and Tsirigos, Konstantinos D. and Vastermark, Ake and Vriend, Gerrit (2015) Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. In: DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION .
Mudgal, Richa and Sandhya, Sankaran and Chandra, Nagasuma and Srinivasan, Narayanaswamy (2015) De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. In: BIOLOGY DIRECT, 10 .
Ramakrishnan, Gayatri and Ochoa-Montano, Bernardo and Raghavender, Upadhyayula S and Mudgal, Richa and Joshi, Adwait G and Chandra, Nagasuma R and Sowdhamini, Ramanathan and Blundell, Tom L and Srinivasan, Narayanaswamy (2015) Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function. In: TUBERCULOSIS, 95 (1). pp. 14-25.
Sudha, Govindarajan and Naveenkumar, Nagarajan and Srinivasan, Narayanaswamy (2015) Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83 (10). pp. 1766-1786.
Kalaivani, Raju and Srinivasan, Narayanaswamy (2015) A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases. In: MOLECULAR BIOSYSTEMS, 11 (4). pp. 1079-1095.
Mudgal, Richa and Sandhya, Sankaran and Kumar, Gayatri and Sowdhamini, Ramanathan and Chandra, Nagasuma R and Srinivasan, Narayanaswamy (2015) NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. In: NUCLEIC ACIDS RESEARCH, 43 (D1). D300-D305.
Ramakrishnan, Gayatri and Chandra, Nagasuma R and Srinivasan, Narayanaswamy (2015) Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv. In: MOLECULAR BIOSYSTEMS, 11 (12). pp. 3316-3331.
Metri, Rahul and Hariharaputran, Sridhar and Ramakrishnan, Gayatri and Anand, Praveen and Raghavender, Upadhyayula S and Ochoa-Montano, Bernardo and Higueruelo, Alicia P and Sowdhamini, Ramanathan and Chandra, Nagasuma R and Blundell, Tom L and Srinivasan, Narayanaswamy (2015) SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. In: DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION .
Lakshmi, Balasubramanian and Mishra, Madhulika and Srinivasan, Narayanaswamy and Archunan, Govindaraju (2015) Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily. In: PLOS ONE, 10 (8).
Rakshambikai, Ramaswamy and Manoharan, Malini and Gnanavel, Mutharasu and Srinivasan, Narayanaswamy (2015) Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates. In: RSC ADVANCES, 5 (32). pp. 25132-25148.
Mahajan, Swapnil and de Brevern, Alexandre G and Sanejouand, Yves-Henri and Srinivasan, Narayanaswamy and Offmann, Bernard (2015) Use of a structural alphabet to find compatible folds for amino acid sequences. In: PROTEIN SCIENCE, 24 (1). pp. 145-153.
Sudha, Govindarajan and Singh, Prashant and Swapna, Lakshmipuram S and Srinivasan, Narayanaswamy (2015) Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. In: PROTEIN SCIENCE, 24 (11). pp. 1856-1873.
Bhat, Prasanna and Shwetha, Shivaprasad and Sharma, Divya Khandige and Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and Das, Saumitra (2015) The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function. In: NUCLEIC ACIDS RESEARCH, 43 (5). pp. 2888-2901.
Bhaskara, Ramachandra M and Padhi, Amrita and Srinivasan, Narayanaswamy (2014) Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: Implications for three-dimensional modeling. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82 (7). pp. 1219-1234.
Gnanavel, Mutharasu and Mehrotra, Prachi and Rakshambikai, Ramaswamy and Martin, Juliette and Srinivasan, Narayanaswamy and Bhaskara, Ramachandra M (2014) CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins. In: BMC BIOINFORMATICS, 15 .
Vishwanath, Sneha and Srinivasan, Narayanaswamy (2014) Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: Scaffolds for promiscuous binding. In: PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 116 (2-3). pp. 151-157.
Mahajan, Swapnil and de Brevern, Alexandre G and Offmann, Bernard and Srinivasan, Narayanaswamy (2014) Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (5). pp. 751-758.
Mudgal, Richa and Sowdhamini, Ramanathan and Chandra, Nagasuma and Srinivasan, Narayanaswamy and Sandhya, Sankaran (2014) Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability. In: JOURNAL OF MOLECULAR BIOLOGY, 426 (4). pp. 962-979.
Ramakrishnan, Gayatri and Chandra, Nagasuma R and Srinivasan, Narayanaswamy (2014) From Workstations to Workbenches: Towards Predicting Physicochemically Viable Protein-Protein Interactions Across a Host and a Pathogen. In: IUBMB LIFE, 66 (11). pp. 759-774.
Rakshambikai, Ramaswamy and Gnanavel, Mutharasu and Srinivasan, Narayanaswamy (2014) Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes. In: PLOS ONE, 9 (9).
Lakshmi, Balasubramanian and Sinduja, Chandrasekaran and Archunan, Govind and Srinivasan, Narayanaswamy (2014) Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure. In: PROTEIN SCIENCE, 23 (6). pp. 843-850.
Joseph, Agnel Praveen and Bhat, Prasanna and Das, Saumitra and Srinivasan, Narayanaswamy (2014) Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA. In: RNA BIOLOGY, 11 (7). pp. 891-905.
Reddy, Uma B and Mullick, Ranajoy and Kumar, Anuj and Sudha, Govindarajan and Srinivasan, Narayanaswamy and Das, Saumitra (2014) Small molecule inhibitors of HCV replication from Pomegranate. In: SCIENTIFIC REPORTS, 4 .
Leonard, Sylvain and Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and Gelly, Jean-Christophe and de Brevern, Alexandre G (2014) mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (4). pp. 661-668.
Sudha, Govindarajan and Nussinov, Ruth and Srinivasan, Narayanaswamy (2014) An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. In: PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 116 (2-3). pp. 141-150.
Bhaskara, Ramachandra M and Mehrotra, Prachi and Rakshambikai, Ramaswamy and Gnanavel, Mutharasu and Martin, Juliette and Srinivasan, Narayanaswamy (2014) The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins. In: MOLECULAR BIOSYSTEMS, 10 (5). pp. 1082-1093.
Gabriel, Nishanth and Hareendran, Sangeetha and Sen, Dwaipayan and Gadkari, Rupali A and Sudha, Govindarajan and Selot, Ruchita and Hussain, Mansoor and Dhaksnamoorthy, Ramya and Samuel, Rekha and Srinivasan, Narayanaswamy and Srivastava, Alok and Jayandharan, Giridhara R (2013) Bioengineering of AAV2 Capsid at Specific Serine, Threonine, or Lysine Residues Improves Its Transduction Efficiency in Vitro and in Vivo. In: HUMAN GENE THERAPY METHODS, 24 (2). 80-U117.
Mahajan, Swapnil and Agarwal, Garima and Iftekhar, Mohammed and Offmann, Bernard and de Brevern, Alexandre G and Srinivasan, Narayanaswamy (2013) DoSA: Database of Structural Alignments. In: DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2013 .
Hansen, Anne-Marie and Chaerkady, Raghothama and Sharma, Jyoti and Diaz-Mejia, Javier J and Tyagi, Nidhi and Renuse, Santosh and Jacob, Harrys KC and Pinto, Sneha M and Sahasrabuddhe, Nandini A and Kim, Min-Sik and Delanghe, Bernard and Srinivasan, Narayanaswamy and Emili, Andrew and Kaper, James B and Pandey, Akhilesh (2013) The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence. In: PLOS PATHOGENS, 9 (6).
Kaushik, Swati and Mutt, Eshita and Chellappan, Ajithavalli and Sankaran, Sandhya and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan (2013) Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage. In: PLOS ONE, 8 (2).
Rakshambikai, Ramaswamy and Srinivasan, Narayanaswamy and Nishant, Koodali Thazath (2013) Structural Insights into Saccharomyces cerevisiae Msh4-Msh5 Complex Function Using Homology Modeling. In: PLOS ONE, 8 (11).
Vendra, Venkata Pulla Rao and Agarwal, Garima and Chandani, Sushil and Talla, Venu and Srinivasan, Narayanaswamy and Balasubramanian, Dorairajan (2013) Structural Integrity of the Greek Key Motif in beta gamma-Crystallins Is Vital for Central Eye Lens Transparency. In: PLOS ONE, 8 (8).
Sen, Dwaipayan and Gadkari, Rupali A and Sudha, Govindarajan and Gabriel, Nishanth and Kumar, Yesupatham Sathish and Selot, Ruchita and Samuel, Rekha and Rajalingam, Sumathi and Ramya, V and Nair, Sukesh C and Srinivasan, Narayanaswamy and Srivastava, Alok and Jayandharan, Giridhara R (2013) Targeted Modifications in Adeno-Associated Virus Serotype 8 Capsid Improves Its Hepatic Gene Transfer Efficiency In Vivo. In: HUMAN GENE THERAPY METHODS, 24 (2). 104-U64.
Bhaskara, Ramachandra M and de Brevern, Alexandre G and Srinivasan, Narayanaswamy (2013) Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31 (12). pp. 1467-1480.
Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and de Brevern, Alexandre G (2012) Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies. In: BIOCHIMIE, 94 (9). pp. 2025-2034.
Joseph, Agnel Praveen and Valadie, Helene and Srinivasan, Narayanaswamy and de Brevern, Alexandre G. (2012) Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes. In: PLOS ONE, 7 (6).
Swapna, Lakshmipuram Seshadri and Srikeerthana, Kuchi and Srinivasan, Narayanaswamy (2012) Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance. In: PLOS ONE, 7 (5).
Swapna, Lakshmipuram S and Mahajan, Swapnil and Brevern, Alexandre G de and Srinivasan, Narayanaswamy (2012) Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. In: BMC Structural Biology, 12 .
Swapna, Lakshmipuram S and Bhaskara, Ramachandra M and Sharma, Jyoti and Srinivasan, Narayanaswamy (2012) Roles of residues in the interface of transient protein-protein complexes before complexation. In: Scientific Reports, 2 .
Amarnath, S and Kawli, Trupti and Mohanty, Smita and Srinivasan, Narayanaswamy and Nanjundiah, Vidyanand (2012) Pleiotropic Roles of a Ribosomal Protein in Dictyostelium discoideum. In: PLOS ONE, 7 (2).
Gadkari, Rupali A. and Srinivasan, Narayanaswamy (2012) Protein-Protein Interactions in Clathrin Vesicular Assembly: Radial Distribution of Evolutionary Constraints in Interfaces. In: PLOS ONE, 7 (2). e31445.
Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and de Brevern, AlexandreG (2012) Cis-trans peptide variations in structurally similar proteins. In: AMINO ACIDS, 43 (3). pp. 1369-1381.
Sudha, Govindarajan and Yamunadevi, Subburaj and Tyagi, Nidhi and Das, Saumitra and Srinivasan, Narayanaswamy (2012) Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR. In: BMC STRUCTURAL BIOLOGY, 12 .
Swapna, Lakshmipuram S and Srinivasan, Narayanaswamy and Robertson, David L and Lovell, Simon C (2012) The origins of the evolutionary signal used to predict protein-protein interactions. In: BMC EVOLUTIONARY BIOLOGY, 12 .
Bhaskara, Ramachandra M and Srinivasan, Narayanaswamy (2011) Stability of domain structures in multi-domain proteins. In: Scientific Reports, 1 .
Krishnadev, Oruganty and Srinivasan, Narayanaswamy (2011) AlignHUSH: Alignment of HMMs using structure and hydrophobicity information. In: BMC Bioinformatics, 12 .
Gelly, Jean-Christophe and Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and de Brevern, Alexandre G (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. In: Nucleic Acids Research, 39 (2). W18-W23.
Agarwal, Garima and Mahajan, Swapnil and Srinivasan, Narayanaswamy and De Brevern, Alexandre G (2011) Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks. In: PLos One, 6 (3).
Martin, Juliette and Anamika, Krishanpal and Srinivasan, Narayanaswamy (2010) Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions. In: PLos One, 5 (9).
Gadkari, Rupali A and Srinivasan, Narayanaswamy (2010) Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures. In: BMC Structural Biology, 10 .
Tyagi, Nidhi and Anamika, Krishanpal and Srinivasan, Narayanaswamy (2010) A Framework for Classification of Prokaryotic Protein Kinases. In: PLos One, 5 (5).
Malshetty, Vidyasagar and Kurthkoti, Krishna and China, Arnab and Mallick, Bratati and Yamunadevi, Subburaj and Sang, Pau Biak and Srinivasan, Narayanaswamy and Nagaraja, Valakunja and Varshney, Umesh (2010) Novel insertion and deletion mutants of RpoB that render Mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription. In: Microbiology, 156 (Part 5). pp. 1565-1573.
Deshmukh, Krupa and Anamika, Krishanpal and Srinivasan, Narayanaswamy (2010) Evolution of domain combinations in protein kinases and its implications for functional diversity. In: Progress in Biophysics and Molecular Biology, 102 (1). pp. 1-15.
Anamika, Krishanpal and Garnier, Nicolas and Srinivasan, Narayanaswamy (2009) Functional diversity of human protein kinase splice variants marks significant expansion of human kinome. In: BMC Genomics, 10 .
Kumar, Anujith and Bhosale, Manoj and Reddy, Surendranath and Srinivasan, Narayanaswamy and Nandi, Dipankar (2009) Importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the M1 family: Thermoplasma acidophilum Tricorn interacting factor F2 and Escherichia coli Peptidase N. In: Biochimie, 91 (9). pp. 1145-1155.
Agarwal, Garima and Rajavel, Malligarjunan and Gopal, Balasubramanian and Srinivasan, Narayanaswamy (2009) Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold. In: PLoS ONE, 4 (5).
Kandathil, Abraham Joseph and Joseph, Agnel Praveen and Kannangai, Rajesh and Srinivasan, Narayanaswamy and Abraham, Oriapadickal Cherian and Pulimood, Susanne Alexander and Sridharan, Gopalan (2009) Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India. In: AIDS Research and Human Retroviruses, 25 (5). pp. 511-519.
Tyagi, Nidhi and Krishnadev, Oruganty and Srinivasan, Narayanaswamy (2009) Prediction of protein-protein interactions between Helicobacter pylori and a human host. In: Molecular BioSystems, 5 (12). pp. 1630-1635.
Anamika, Krishanpal and Martin, Juliette and Srinivasan, Narayanaswamy (2008) Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations. In: BMC Genomics, 9 . 625-1-625-16.
Talla, Venu and Srinivasan, Narayanaswamy and Balasubramanian, Dorairajan (2008) Visualization of in situ intracellular aggregation of two cataract-associated human gamma-crystallin mutants: Lose a tail, lose transparency. In: Investigative Ophthalmology & Visual Science, 49 (8). pp. 3483-3490.
Pantakani, Krishna DV and Swapna, Lakshmipuram S and Srinivasan, Narayanaswamy and Mannan, Ashraf U (2008) Spastin oligomerizes into a hexamer and the mutant spastin (E442Q) redistribute the wild-type spastin into filamentous microtubule. In: Journal of Neurochemistry, 106 (2). pp. 613-624.
Sandhya, Sankaran and Pankaj, Barah and Govind, Madabosse Kande and Offmann, Bernard and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan (2008) CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. In: BMC Structural Biology, 8 (28).
Jhingran, Anupam and Padmanabhan, Prasad K and Singh, Sushma and Anamika, Krishanpal and Bakre, Abhijeet A and Bhattacharya, Sudha and Bhattacharya, Alok and Srinivasan, Narayanaswamy and Madhubala, Rentala (2008) Characterization of the Entamoeba histolytica Ornithine Decarboxylase-Like Enzyme. In: PLoS Neglected Tropical Diseases, 2 (1).
Padmanabhan, Prasad K and Mukherjee, Angana and Singh, Sushma and Chattopadhyaya, Swati and Gowri, Venkataraman S and Myler, Peter J and Srinivasan, Narayanaswamy and Madhubala, Rentala (2005) Glyoxalase I from Leishmania donovani: A potential target for anti-parasite drug. In: Biochemical and Biophysical Research Communications, 337 (4). pp. 1237-1248.
Bhadra, Rana and Srinivasan, Narayanaswamy and Pandit, Shashi B (2005) A New Domain Family in the Superfamily of Alkaline Phosphatases. In: In Silico Biology, 5 (4). pp. 379-387.
Namboori, Seema and Srinivasan, Narayanaswamy and Pandit, Shashi B (2004) Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures. In: In Silico Biology, 4 . pp. 445-460.
Namboori, Seema and Mhatre, Natasha and Sujatha, Sentivel and Srinivasan, Narayanaswamy and Pandit, Shashi Bhushan (2004) Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. In: Journal of Biosciences, 29 (3). pp. 245-259.
Pudi, Renuka and Abhiman, Saraswathi and Srinivasan, Narayanaswamy and Das, Saumitra (2003) Hepatitis C Virus Internal Ribosome Entry Site-mediated Translation Is Stimulated by Specific Interaction of Independent Regions of Human La Autoantigen. In: Journal of Biological Chemistry, 278 (14). pp. 12231-12240.
Krupa, Ananth and Sandhya, Kumaraswamy and Srinivasan, Narayanaswamy and Jonnalagadda, Sobhanaditya (2003) A conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer. In: Trends in Biochemical Sciences, 28 (1). pp. 9-12.
Sehrawat, Seema and Srinivasan, Narayanaswamy and Gopinathan, Karumathil P (2002) Functional characterization and structural modelling of late gene expression factor 4 from Bombyx mori nucleopolyhedrovirus. In: Biochemical Journal, 368 . pp. 159-169.
Gupta, Surbhi and Pandit, Shashi B and Srinivasan, Narayanaswamy and Chatterji, Dipankar (2002) Proteomics analysis of carbon-starved Mycobacterium smegmatis: Induction of Dps-like protein. In: Protein Engineering, 15 (6). pp. 503-511.
Newbold, Richard J and Deery, Evelyne C and Walker, Caroline E and Wilkie, Susan E and Srinivasan, Narayanaswamy and Hunt, David M (2001) The destabilization of human GCAP1 by a proline to leucine mutation might cause cone-rod dystrophy. In: Human Molecular Genetics, 10 (1). pp. 47-54.
Srinivasan, Narayanaswamy (2019) Chandrasekharan Ramakrishnan (1939-2019): The student behind the Ramachandran map IN MEMORIAM. In: PROTEIN SCIENCE .
Orozco, Modesto and Srinivasan, Narayanaswamy (2016) Editorial overview: Theory and simulation. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 37 . IV-V.
Mehrotra, Prachi and Bhaskara, Ramachandra M and Gnanavel, Mutharasu and Rakshambikai, Ramaswamy and Martin, Juliette and Srinivasan, Narayanaswamy (2015) Classification of protein sequences with special references to multi-domain systems. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). p. 110.
Holliday, Gemma L and Bairoch, Amos and Bagos, Pantelis G and Chatonnet, Arnaud and Craik, David J and Finn, Robert D and Henrissat, Bernard and Landsman, David and Manning, Gerard and Nagano, Nozomi and O'Donovan, Claire and Pruitt, Kim D and Rawlings, Neil D and Saier, Milton and Sowdhamini, Ramanathan and Spedding, Michael and Srinivasan, Narayanaswamy and Vriend, Gert and Babbitt, Patricia C and Bateman, Alex (2015) Key challenges for the creation and maintenance of specialist protein resources. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83 (6). pp. 1005-1013.
