Items where Author is "Sowdhamini, Ramanathan"

Article

Kalmankar, Neha V. ; Venkatesan, Radhika ; Balaram, Padmanabhan ; Sowdhamini, Ramanathan (2020) Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis Scientific Reports, 10 (1). ISSN 2045-2322

Gupte, Tejas M. ; Haque, Farah ; Gangadharan, Binnu ; Sunitha, Margaret S. ; Mukherjee, Souhrid ; Anandhan, Swetha ; Rani, Deepa Selvi ; Mukundan, Namita ; Jambekar, Amruta ; Thangaraj, Kumarasamy ; Sowdhamini, Ramanathan ; Sommese, Ruth F. ; Nag, Suman ; Spudich, James A. ; Mercer, John A. (2015) Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies Journal of Biological Chemistry, 290 (11). pp. 7003-7015. ISSN 0021-9258

Mudgal, Richa ; Sandhya, Sankaran ; Kumar, Gayatri ; Sowdhamini, Ramanathan ; Chandra, Nagsuma R. ; Srinivasan, Nrayanaswamy (2015) NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection Nucleic Acids Research, 43 (D1). pp. D300-D305. ISSN 0305-1048

Ramakrishnan, Gayatri ; Ochoa-Montaño, Bernardo ; Raghavender, Upadhyayula S. ; Mudgal, Richa ; Joshi, Adwait G. ; Chandra, Nagasuma R. ; Sowdhamini, Ramanathan ; Blundell, Tom L. ; Srinivasan, Narayanaswamy (2015) Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function Tuberculosis, 95 (1). pp. 14-25. ISSN 1472-9792

Metri, Rahul ; Hariharaputran, Sridhar ; Ramakrishnan, Gayatri ; Anand, Praveen ; Raghavender, Upadhyayula S. ; Ochoa-Montaño, Bernardo ; Higueruelo, Alicia P. ; Sowdhamini, Ramanathan ; Chandra, Nagasuma R. ; Blundell, Tom L. ; Srinivasan, Narayanaswamy (2015) SInCRe—structural interactome computational resource for Mycobacterium tuberculosis Database, 2015 (1). Article ID bav060. ISSN 1758-0463

Mudgal, Richa ; Sowdhamini, Ramanathan ; Chandra, Nagasuma ; Srinivasan, Narayanaswamy ; 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 Journal of Molecular Biology, 426 (4). pp. 962-979. ISSN 0022-2836

Shameer, Khader ; Shingate, Prashant N. ; Manjunath, S. C. P. ; Karthika, M. ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2011) 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping Database, 2011 . pp. 1-15. ISSN 1758-0463

Shameer, Khader ; Pugalenthi, Ganesan ; Kandaswamy, Krishna Kumar ; Sowdhamini, Ramanathan (2011) 3dswap-pred: prediction of 3D domain swapping from protein sequence using random forest approach Protein and Peptide Letters, 18 (10). pp. 1010-1020. ISSN 0929-8665

Kalaimathy, Singarevelu ; Sowdhamini, Ramanathan ; Kanagarajadurai, Karuppiah (2011) Critical assessment of structure-based sequence alignment methods at distant relationships Briefings in Bioinformatics, 12 (2). pp. 163-175. ISSN 1467-5463

Nagarathnam, Balasubramanian ; Kannan, Sankar ; Dharnidharka, Varadhan ; Balakrishnan, Veluchamy ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2011) Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters Bioinformation, 7 (1). pp. 15-20. ISSN 0973-2063

Shameer, Khader ; Pugalenthi, Ganesan ; Kandaswamy, Krishna Kumar ; Suganthan, Ponnuthurai N. ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2010) Insights into protein sequence and structure-derived features mediating 3D domain swapping mechanism using support vector machine based approach Bioinformatics and Biology Insights (4). pp. 33-42. ISSN 1177-9322

Sowdhamini, Ramanathan ; Parthiban, Marimuthu ; Koshy, Caroline (2010) 100 ns molecular dynamics simulations to study intramolecular conformational changes in bax Journal of Biomolecular Structure and Dynamics, 28 (1). pp. 71-83. ISSN 0739-1102

Sundaramurthy, Pandurangan ; Shameer, Khader ; Sreenivasan, Raashi ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2010) HORI: a web server to compute Higher Order residue interactions in protein structures BMC Bioinformatics, 11 (1). No pp. given. ISSN 1471-2105

Parthiban, Marimuthu ; Shanmughavel, Piramanayagam ; Sowdhamini, Ramanathan (2010) In silico point mutation and evolutionary trace analysis applied to nicotinic acetylcholine receptors in deciphering ligand-binding surfaces Journal of Molecular Modeling, 16 (10). pp. 1651-1670. ISSN 1610-2940

Shameer, Khader ; Madan, Lalima L. ; Veeranna, Shivamurthy ; Gopal, Balasubramanian ; Sowdhamini, Ramanathan (2010) PeptideMine - a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes BMC Bioinformatics, 11 . pp. 473_1-473_14. ISSN 1471-2105

Anbazhagan, Padmanabhan ; Purushottam, Meera ; Kumar, Kiran ; Mukherjee, Odity ; Jain, Sanjeev ; Sowdhamini, Ramanathan (2010) Phylogenetic analysis and selection pressures of 5-HT receptors in human and non-human primates: receptor of an ancient neurotransmitter Journal of Biomolecular Structure and Dynamics, 27 (5). pp. 581-598. ISSN 0739-1102

Shameer, Khader ; Nagarajan, Paramasivam ; Gaurav, Kumar ; Sowdhamini, Ramanathan (2009) 3PFDB - a database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach BioData Mining, 2 . pp. 8_1-8_10. ISSN 1756-0381

Sundaramurthy, Pandurangan ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2009) Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: a systems approach Bioinformation, 3 (6). pp. 244-249. ISSN 0973-2063

Sundaramurthy, Pandurangan ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2009) Computational prediction and analysis of impact of the cross‐talks between JNK and P38 kinase cascades Bioinformation, 3 (6). pp. 250-254. ISSN 0973-2063

Sandhya, Sankaran ; Rani, Saane Sudha ; Pankaj, Barah ; Govind, Madabosse Kande ; Offmann, Bernard ; Srinivasan, Narayanaswamy ; Sowdhamini, Ramanathan (2009) Length variations amongst protein domain superfamilies and consequences on structure and function PLoS ONE, 4 (3). No PP. Given.. ISSN 1932-6203

Kanagarajadurai, Karuppiah ; Malini, Manoharan ; Bhattacharya, Aditi ; Panicker, Mitradas M. ; Sowdhamini, Ramanathan (2009) Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT_2A) receptor for the identification of hotspots for ligand binding Molecular BioSystems, 5 (12). pp. 1877-1888. ISSN 1742-206X

Vyas, Neha ; Goswami, Debanjan ; Manonmani, A. ; Sharma, Pranav ; Ranganath, Hassan Annegowda ; VijayRaghavan, Krishnaswamy ; Shashidhara, L. S. ; Sowdhamini, Ramanathan ; Mayor, Satyajit (2008) Nanoscale organization of hedgehog is essential for long-range signaling Cell, 133 (7). pp. 1214-1227. ISSN 0092-8674

Sandhya, Sankaran ; Pankaj, Barah ; Govind, Madabosse Kande ; Offmann, Bernard ; Srinivasan, Narayanaswamy ; 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 BMC Structural Biology, 8 (28). No PP. Given.. ISSN 1472-6807

Anbazhagan, Padmanabhan ; Purushottam, Meera ; Kiran Kumar, H. B. ; Kubendran, Shobana ; Mukherjee, Odity ; Brahmachari, Samir Kumar ; Jain, Sanjeev ; Sowdhamini, Ramanathan (2008) Evolutionary analysis of PHLPP1 gene in humans and non-human primates Bioinformation, 2 (10). pp. 471-474. ISSN 0973-2063

Reddy, Chilamakuri C. S. ; Shameer, Khader ; Offmann, Bernard O. ; Sowdhamini, Ramanathan (2008) PURE: a webserver for the prediction of domains in unassigned regions in proteins BMC Bioinformatic, 9 . pp. 281_1-281_8. ISSN 1471-2105

Sundar, Ambika Shyam ; Varghese, Susan Mary ; Shameer, Khader ; Karaba, Nataraja ; Udayakumar, Makarla ; Sowdhamini, Ramanathan (2008) STIF: identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana Bioinformation, 2 (10). pp. 431-437. ISSN 0973-2063

Kanagarajadurai, Karuppiah ; Sowdhamini, Ramanathan (2008) Sequence and structural analyses of interleukin-8-like chemokine superfamily In Silico Biology, 8 (3-4). pp. 307-330. ISSN 1386-6338

Metpally, Raghu Prasad Rao ; Vigneshwar, Ramakrishnan ; Sowdhamini, Ramanathan (2007) Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis Journal of Biosciences, 32 (1). pp. 43-50. ISSN 0250-5991

Shameer, Khader ; Sowdhamini, Ramanathan (2007) IWS: integrated web server for protein sequence and structure analysis Bioinformation, 2 (3). pp. 86-90. ISSN 0973-2063

Reddy, Sekhar Chilamakuri C. ; Bernard, Offmann ; Sowdhamini, Ramanathan ; Shameer, Khader (2007) PURE: a web server for querying the relationship between pre-existing domains and unassigned regions in proteins Nature . pp. 1-15. ISSN 0028-0836

Khajamohiddin, Syed ; Babu, Pakala Suresh ; Chakka, Deviprasanna ; Merrick, Mike ; Bhaduri, Anirban ; Sowdhamini, Ramanathan ; Siddavattam, Dayananda (2006) A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551 Biochemical and Biophysical Research Communications, 351 (3). pp. 675-681. ISSN 0006-291X

Reddy, Chandrashekar ; Manonmani, Arunachalam ; Babu, Meenakshi ; Sowdhamini, Ramanathan (2006) Enhanced structure prediction of gene products containing class III adenylyl cyclase domains In Silico Biology, 6 (5). pp. 351-362. ISSN 1386-6338

Chakrabarti, Saikat ; Manohari, Gowri ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2006) SSToSS - sequence-structural templates of single-member superfamilies In Silico Biology, 6 (4). pp. 311-319. ISSN 1386-6338

Blaise, Mathias-Costa ; Sowdhamini, Ramanathan ; Pradhan, Nithyananda (2005) Comparative analysis of different competitive antagonists interaction with NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor Journal of Molecular Modeling, 11 (6). pp. 489-502. ISSN 1610-2940

Metpally, Raghu Prasad Rao ; Sowdhamini, Ramanathan (2005) Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors BMC Genomics, 6 . pp. 106_1-106_20. ISSN 1471-2164

Pugalenthi, Ganesan ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2005) DIAL: a web-based server for the automatic identification of structural domains in proteins Nucleic Acids Research, 33 (S-2). pp. W130-W132. ISSN 0305-1048

Gaurav, Kumar ; Gupta, Nitin ; Sowdhamini, Ramanathan (2005) FASSM: enhanced function association in whole genome analysis using sequence and structural motifs In Silico Biology, 5 (5-6). pp. 425-438. ISSN 1386-6338

Pugalenthi, Ganesan ; Bhaduri, Anirban ; Sowdhamini, Ramanathan (2005) GenDiS: Genomic Distribution of protein structural domain Superfamilies Nucleic Acids Research, 33 (S-1). pp. D252-D255. ISSN 0305-1048

Metpally, Raghu Prasad Rao ; Sowdhamini, Ramanathan (2005) Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis BMC Evolutionary Biology, 5 . pp. 41_1-41_10. ISSN 1471-2148

Blaise, Mathias-Costa ; Bhattacharyya, Dananjay ; Sowdhamini, Ramanathan ; Pradhan, Nityananda (2005) Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: a molecular dynamics study Journal of Biomolecular Structure and Dynamics, 22 (4). pp. 399-410. ISSN 0739-1102

Blaise, Mathias-Costa ; Sowdhamini, Ramanathan ; Rao, Metpally Raghu Prasad ; Pradhan, Nithyananda (2004) Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits Journal of Molecular Modeling, 10 (5-6). pp. 305-316. ISSN 1610-2940

Chakrabarti, Saikat ; Bhardwaj, Nitin ; Anand, Prem A. ; Sowdhamini, Ramanathan (2004) Improvement of alignment accuracy utilizing sequentially conserved motifs BMC Bioinformatics, 5 . pp. 167_1-167_12. ISSN 1471-2105

Chakrabarti, Saikat ; John, Jaisurya ; Sowdhamini, Ramanathan (2004) Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints Journal of Molecular Modeling, 10 (1). pp. 69-75. ISSN 1610-2940

Bhaduri, Anirban ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2004) PASS2: an automated database of protein alignments organised as structural superfamilies BMC Bioinformatics, 5 . pp. 35_1-35_7. ISSN 1471-2105

Bhaduri, Anirban ; Krishnaswamy, Lakshminarasimhan ; Ullal, Gautam R. ; Panicker, Mitradas M. ; Sowdhamini, Ramanathan (2003) Fold prediction and comparative modeling of Bdm1: a probable α/β hydrolase associated with hot water epilepsy Journal of Molecular Modeling, 9 (1). pp. 3-8. ISSN 1610-2940

May, Alex C. W. ; Johnson, Mark S. ; Rufino, Stephen D. ; Wako, Hiroshi ; Zhu, Zhan-Yang ; Sowdhamini, Ramanathan ; Srinivasan, Narayanaswamy ; Rodionov, Michael A. ; Blundell, Tom L. ; Dover, G. A. (1994) The recognition of protein structure and function from sequence: adding value to genome data [and discussion] Philosophical Transactions: Biological Sciences, 344 (1310). pp. 373-381. ISSN 0962-8436

Johnson, Mark S. ; Srinivasan, Narayanaswamy ; Sowdhamini, Ramanathan ; Blundell, Tom L. (1994) Knowledge-based protein modeling Critical Reviews in Biochemistry and Molecular Biology, 29 (1). pp. 1-68. ISSN 1040-9238

Overington, John P. ; Zhu, Zhan‑Yang ; Šali, Andrej ; Johnson, Mark S. ; Sowdhamini, Ramanathan ; Louie, Gordon V. ; Blundell, Tom L. (1993) Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins Biochemical Society Transactions, 21 (3). pp. 597-604. ISSN 0300-5127

Srinivasan, N. ; Sowdhamini, Ramanathan ; Ramakrishnan, Chandrashekharan ; Balaram, Padmanabhan (1991) Analysis of short loops connecting secondary structural elements in proteins Molecular Conformation and Biological Interactions . pp. 59-73.

Ramakrishnan, Chandrashekharan ; Sowdhamini, Ramanathan ; Balaram, Padmanabhan (1988) Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear overhauser effects Collection of Czechoslovak Chemical Communications, 53 (11). pp. 2801-2809. ISSN 0010-0765