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Items where Subject is "Division of Information Sciences > BioInformatics Centre"

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Conference Paper

Ganapathiraju, Madhavi K and Weisser, D and Rosenfeld, R and Carbonell, J and Reddy, R and Klein-Seetharaman, J (2002) Comparative n-gram analysis of whole-genome sequences. In: HLT02: Human Language Technologies, April-2002, San Diego, California, USA.

Journal Article

Muktha, B and Srinivas, O and Amresh, MR and Row, Guru TN and Jayaraman, N and Sekar, K (2004) Corrigendum to 'The crystal structure of 1,2,3,4,6-penta-O-benzoyl-a-D-mannopyranose: observation of $C-H\cdot\cdot\cdot{\pi}$ interaction as a surrogate to $O-H\cdot\cdot\cdot{O}$ interaction of a free sugar’. In: Carbohydrate Research, 339 (2). pp. 435-436.

Acharya, Rudresh and Gupta, Madhvi and Ramakumar, Suryanarayanarao and Ramagopal, Udupi A and Chauhan, Virander S (2007) Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide. In: BMC Structural Biology, 7 (51). pp. 1-9.

Ajees, Abdul A and Sekar, K and Parthasarathy, S and Balakrishna, K (2000) Crystal and Molecular Structure of Desmodin. In: Crystal Research and Technology, 35 (9). pp. 1117-1123.

Ajees, Abdul A and Sekar, K and Marappan, M and Kandaswamy, M (2001) 4-tert-Butyl-2,6-bis(piperidinomethyl)phenol. In: Acta Crystallographica Section E Structure Reports online, 57 (9). o878-o880.

Ajees, Abdul A and Sekar, K and Parthasarathy, S and Schenk, H and Epe, B and Mondon, A (2001) Tricoccin R6. In: Acta Crystallographica Section E: Structure Reports Online, 57 (2). o116-o117.

Amara, Rama Rao and Satchidhanandam, Vijaya (1996) Analysis of a Genomic DNA Expression Library of Mycobacterium tuberculosis Using Tuberculosis Patient Sera: Evidence for Modulation of Host Immune Response. In: Infection and Immunity, 64 (09). pp. 3765-3771.

Ananthalakshmi, Parthiban and Samayamohan, Krishnan and Chokalingam, Chellapandi and Mayilarasi, Chandran and Sekar, Kanagaraj (2005) PSST-2.0: Protein Data Bank Sequence Search Tool. In: Applied Bioinformatics, 4 (2). pp. 141-145.

Ananthalakshmi, P and Kumar, Kiran M and Jeyasimhan, M and Sumathi, K and Sekar, K (2005) Fragment Finder: A Web-based Software to Identify Similar three-dimensional Structural Motif. In: Nucleic Acids Research, 33 (Suppl.). W85-W88.

Anilkumar, HG and Yathirajan, HS and Narasimhamurthy, T and Vijay, T and Rathore, RS (2005) Intermolecularly associated carboxylic acid dimers in the supramolecular assembly of 2-(2-phenylethyl)benzoic acid. In: Acta Crystallographica Section E: Structure Reports Online, 61 (Part 8). o2704-o2705.

Arora, Ashish and Chandra, Nagasuma R and Das, Amit and Gopal, Balasubramanian and Mande, Shekhar C and Prakash, Balaji and Ramachandran, Ravishankar and Sankaranarayanan, Rajan and Sekar, K and Suguna, Kaza and Tyagi, Anil K and Vijayan, Mamannamana (2011) Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts. In: Tuberculosis, 91 (5, SI). pp. 456-468.

Arora, Pankhuri and Dixit, Narendra M (2009) Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers. In: Plos Computational Biology, 5 (3). pp. 1-10.

Babu, Venkatesh and Uthayakumar, M and Vaishnavi, Kirti M and Senthilkumar, R and Shankar, M and Archana, C and Priya, Sathya S and Sekar, Kanagaraj (2011) RPS: Repeats in Protein Sequences. In: Journal of Applied Crystallography, 44 (Part 3). pp. 647-650.

Bagaria, A and Ramakumar, S and Gupta, M and Chauhan, VS (2005) Cyclo(L-leucyl-$\alpha$,$\beta$-dehydrophenylalanine): the first diketopiperazine containing an $\alpha$,$\beta$-dehydrophenylalanine residue. In: Acta crystallographica. Section C, Crystal structure communications, 61 (3). pp. 174-176.

Bagaria, Ashima and Surendranath, Kalpana and Ramagopal, Udupi A and Ramakumar, Suryanarayanarao and Karande, Anjali A (2006) Structure-Function Analysis and Insights into the Reduced Toxicity of Abrus precatorius Agglutinin I in Relation to Abrin. In: Journal of Biological Chemistry, 281 (45). pp. 34465-34474.

Bairagya, HR and Mukhopadhyay, BP and Sekar, K (2009) An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II (Human): Recognition of Cofactor and Substrate to Catalytic Arg 322. In: Journal of Biomolecular Structure & Dynamics, 27 (2). pp. 149-158.

Bairagya, Hridoy R and Mukhopadhyay, Bishnu P and Sekarz, K (2009) Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II. In: Journal of Biomolecular Structure & Dynamics, 26 (4). pp. 497-507.

Balagam, Rajesh and Singh, Vasantika and Sagi, Aparna Raju and Dixit, Narendra M (2011) Taking Multiple Infections of Cells and Recombination into Account Leads to Small Within-Host Effective-Population-Size Estimates of HIV-1. In: PLos One, 6 (1).

Balamurugan, B and Mohan, Samaya K and Ramesh, J and Roshan, Md MNA and Sumathi, K and Sekar, K (2005) SSEP-2.0: Secondary Structural Elements of Proteins. In: Acta Crystallographica Section D-Biological Crystallography, 61 . pp. 634-636.

Balamurugan, B and Roshan, Md MNA and Hameed, Shaahul B and Sumathi, K and Senthilkumar, R and Udayakumar, A and Babu, Venkatesh KH and Kalaivani, M and Sowmiya, G and Sivasankari, P and Saravanan, S and Ranjani, Vasuki C and Gopalakrishnan, K and Selvakumar, KN and Jaikumar, M and Brindha, T and Michael, Daliah and Sekar, K (2007) PSAP: protein structure analysis package. In: Journal of Applied Crystallography, 40 . pp. 773-777.

Banerjee, Nirjhar and Chidambarathanu, N and Michael, Daliah and Balakrishnan, N and Sekar, K (2008) An algorithm to find all identical internal sequence repeats. In: Current Science, 95 (2). pp. 188-195.

Bansal, Manju (2003) DNA structure: Revisiting the Watson–Crick double helix. In: Current Science, 85 (11). pp. 1556-1563.

Bhagavat, Raghu and Saqib, Asma and Karigar, Chandrakant (2012) Molecular Docking Studies of Novel Palmitoyl-ligands for Cyclooxygenase-2. In: CHEMICAL BIOLOGY & DRUG DESIGN, 79 (6). pp. 1043-1048.

Bharath, Srinivas MM and Chandra, Nagasuma R and Rao, MRS (2002) Prediction of an HMG-box fold in the C-terminal domain of histone H1: Insights into its role in DNA condensation. In: Proteins: Structure, Function, and Genetics, 49 (1). pp. 71-81.

Bharath, Srinivas MM and Ramesh, Sneha and Chandra, Nagasuma R and Rao, MRS (2002) Identification of a 34 Amino Acid Stretch within the C-Terminus of Histone H1 As the DNA-Condensing Domain by Site-Directed Mutagenesis. In: Biochemistry, 41 (24). 7617 -7627.

Bhardwaj, Amit and Leelavathi, Sadhu and Mazumdar-Leighton, Sudeshna and Ghosh, Amit and Ramakumar, Suryanarayanarao and Reddy, Vanga S (2010) The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions. In: PLos One, 5 (6).

Bhardwaj, Anshu and Scaria, Vinod and Raghava, Gajendra Pal Singh and Lynn, Andrew Michael and Chandra, Nagasuma and Banerjee, Sulagna and Raghunandanan, Muthukurussi V and Pandey, Vikas and Taneja, Bhupesh and Yadav, Jyoti and Dash, Debasis and Bhattacharya, Jaijit and Misra, Amit and Kumar, Anil and Ramachandran, Srinivasan and Thomas, Zakir and Brahmachari, Samir K (2011) Open source drug discovery- A new paradigm of collaborative research in tuberculosis drug development. In: Tuberculosis, 91 (5, SI). pp. 479-486.

Bhargavi, Ramya G and Sheik, SS and Velmurugan, D and Sekar, K (2003) Side-chain conformation angles of amino acids: effect of temperature factor cut-off. In: Journal of Structural Biology, 143 (3). pp. 181-184.

Bhattacharya, Sourangshu and Bhattacharyya, Chiranjib and Chandra, Nagasuma R (2007) Comparison of protein structures by growing neighborhood alignments. In: BMC Bioinformatics, 8 (77).

Bhattacharya, Sourangshu and Bhattacharyya, Chiranjib and Chandra, Nagasuma R (2006) Projections for fast protein structure retrieval. In: BMC Bioinformatics, 7 . S5.

Bhavani, S and Nagargadde, A and Thawani, A and Sridhar, V and Chandra, N (2006) Substructure-Based Support Vector Machine Classifiers for Prediction of Adverse Effects in Diverse Classes of Drugs. In: Journal of Chemical Information and Modeling, 46 (6). pp. 2478-2486.

Chaitra, MG and Shaila, MS and Chandra, NR and Nayak, R (2008) HLA-A*0201-restricted Cytotoxic T-cell Epitopes in Three PE/PPE Family Proteins of Mycobacterium tuberculosis. In: Scandinavian Journal of Immunology, 67 (4). pp. 411-417.

Chaitra, GM and Hariharaputran, Sridhar and Chandra, Nagasuma R and Shaila, MS and Nayak, R (2005) Defining putative T cell epitopes from PE and PPE families of proteins of Mycobacterium tuberculosis with vaccine potential. In: Vaccine, 23 (10). pp. 1265-1272.

Chandra, Nagasuma (2009) Computational systems approach for drug target discovery. In: Expert Opinion on Drug Discovery, 4 (12). pp. 1221-1236.

Chandra, Nagasuma and Kumar, Dhiraj and Rao, Kanury (2011) Systems biology of tuberculosis. In: Tuberculosis, 91 (5, SI). pp. 487-496.

Chandra, Nagasuma R and Kumar, Nirmal and Justin, Jeyakani and Singh, Desh Deepak and Gowda, Sharan B and Prathima, MN (2006) Lectindb: a plant lectin database. In: Glycobiology, 16 (10). pp. 938-946.

Chandra, Nagasuma R and Prabu, MM and Suguna, K and Vijayan, M (2001) Structural Similarity and Functional Diversity in Proteins containing the Legume Lectin Fold. In: Protien Engineering, 14 (11). pp. 857-866.

Chetan, Nag and Praveen, Karanth K and Vasudeva, Gururaja Kotambylu (2014) Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach. In: PLOS ONE, 9 (2).

Christlet, T Hema Thanka and Biswas, M and Veluraja, K (1999) A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences. In: Acta Crystallographica Section D Biological Crystallography, 55 (8). pp. 1414-1420.

Das, Soma and Laxminarayana, Suhas Venkataramana and Chandra, Nagasuma and Ravi, Vasanthapuram and Desai, Anita (2009) Heat shock protein 70 on Neuro2a cells is a putative receptor for Japanese encephalitis virus. In: Virology, 385 (1). pp. 47-57.

Dash, Banaja P and Mukherjee, Sumanto and Suhas, VL and Chandra, Nagasuma (2007) Interaction Profiling of T-Cell Epitopes with MHC-Class I Molecules. In: Protein and Peptide Letters, 14 (6). pp. 557-564.

Datta, S and Ganesh, N and Chandra, Nagasuma R and Muniyappa, K and Vijayan, M (2003) Structural studies on MtRecA-nucleotide complexes: Insights into DNA and nucleotide binding and the structural signature of NTP recognition. In: Proteins: Structure, Function, and Genetics, 50 . pp. 474-485.

Datta, S and Krishna, R and Ganesh, N and Chandra, Nagasuma R and Muniyappa, K and Vijayan, M (2003) Crystal Structures of Mycobacterium smegmatis RecA and Its Nucleotide Complexes. In: Journal of Bacteriology, 185 . pp. 4280-4284.

Dhanasekaran, Shanmugham and Chandra, Nagasuma R and Sagar, Chandrasekhar BK and Rangarajan, Pundi N and Padmanaban, Govindarajan (2004) $\delta$-Aminolevulinic Acid Dehydratase from Plasmodium falciparum. In: Journal of Biological Chemistry, 279 (8). pp. 6934-6942.

Dixit, Narendra M (2008) Advances in the Mathematical Modelling of Hepatitis C Virus Dynamics. In: Journal of the Indian Institute of Science, 88 (1). pp. 37-43.

Fernando, SA and Selvarani, P and Das, Soma and Kumar, Kiran Ch and Mondal, Sukanta and Ramakumar, S and Sekar, K (2004) THGS:a web-based database of Transmembrane Helices in Genome Sequences. In: Nucleic Acids Research, 32 . D125-D128.

Gadhamsetty, Saikrishna and Dixit, Narendra M (2010) Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model. In: Journal of Virology, 84 (19). pp. 10230-10240.

Gangadhar, Vidya and Jeyakani, Justin J and Shaila, MS and Nayak, Rabindranath and Chandra, Nagasuma (2007) Perpetuation of immunological memory through common MHC-I binding modes of peptidomimic and antigenic peptides. In: Biochemical and Biophysical Research Communications, 364 (2). pp. 308-312.

Gopalakrishnan, K and Sheik, SS and Ranjani, Vasuki C and Udayakumar, A and Sekar, K (2007) Conformational Angles Database (CADB-3.0). In: Protein and Peptide Letters, 14 (7). pp. 665-668.

Gopalakrishnan, K and Sowmiya, G and Sheik, SS and Sekar, K (2007) Ramachandran Plot on The Web (2.0). In: Protein and Peptide Letters, 14 (7). pp. 669-671.

Gupta, Kshitiz and Thomas, Dina and Vidya, SV and Venkatesh, KV and Ramakumar, Suryanarayanarao (2005) Detailed protein sequence alignment based on Spectral Similarity Score (SSS). In: BMC Bioinformatics, 6 (105). pp. 1-16.

Gupta, Prabuddha and Rajeswari, Haryadi and Arumugam, Muthu and Mishra, Saurabh and Bhagavat, Raghu and Anand, Praveen and Chandra, Nagasuma R and Srinivasan, Ramanujam and Indi, Shantinath and Ajitkumar, Parthasarathi (2010) Mycobacterium tuberculosis FtsZ requires at least one arginine residue at the C-terminal end for polymerization in vitro. In: Acta Biochimica et Biophysica Sinica, 42 (1). pp. 58-69.

Gupta, Vikas and Prakash, Udaya NA and Lakshmi, V and Boopathy, R and Jeyakanthan, J and Velmurugan, D and Sekar, K (2010) Recognition of active and inactive catalytic triads: A template based approach. In: International Journal of Biological Macromolecules, 46 (3). pp. 317-323.

Hemavathi, K and Kalaivani, M and Udayakumar, A and Sowmiya, G and Jeyakanthan, J and Sekar, K (2010) MIPS: metal interactions in protein structures. In: Journal of Applied Crystallography, 43 (Part 1). pp. 196-199.

Hussain, ASZ and Kumar, Kiran Ch and Rajesh, CK and Sheik, SS and Sekar, K (2003) SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules. In: Nucleic Acids Research, 31 (13). pp. 3356-3558.

Jain, Rinku and Ramakumar, S (1999) Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution. In: Physica A: Statistical Mechanics and its Applications, 273 (3-4). pp. 476-485.

Jayalakshmi, J and Mridula, P and Sekar, K and Vaijayanthimala, S and Velmurugan, D (2006) Interaction of water molecules in non-identical protein structures. In: aniIndian Journal of Chemistry Sect. A: Inorgc, Bio-inorganic, Physical, Theoretical & Analytical, 45 (1). pp. 159-162.

Jeyakanthan, Jeyaraman and Kanaujia, Shankar Prasad and Nishida, Yuya and Nakagawa, Noriko and Praveen, Surendran and Shinkai, Akeo and Kuramitsu, Seiki and Yokoyama, Shigeyuki and Sekar, Kanagaraj (2010) Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5. In: Acta Crystallographica Section D Biological Crystallography, 66 (Part 2). pp. 116-124.

Jeyaprakash, Arockia A and Jayashree, G and Mahanta, SK and Swaminathan, CP and Sekar, K and Surolia, A and Vijayan, M (2005) Structural Basis for the Energetics of Jacalin-Sugar Interactions: Promiscuity Versus Specificity. In: Journal of Molecular Biology, 347 (1). pp. 181-188.

Jeyaprakash, Arockia A and Katiyar, S and Swaminathan, CP and Sekar, K and Surolia, A and Vijayan, M (2003) Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study. In: Journal of Molecular Biology, 332 (1). pp. 217-228.

Jeyaprakash, Arockia A and Rani, Geetha P and Reddy, Banuprakash G and Banumathi, S and Betzel, C and Sekar, K and Surolia, A and Vijayan, M (2002) Crystal Structure of the Jacalin–T-antigen Complex and a Comparative Study of Lectin–T-antigen Complexes. In: Journal of Molecular Biology, 321 (4). pp. 637-645.

Kalidas, Yeturu and Chandra, Nagasuma (2008) PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. In: Journal of Structural Biology, 161 (1). 31 - 42.

Kalidas, Yeturu and Chandra, Nagasuma (2008) PocketDepth:A new depth based algorithm for identification of ligand binding sites in proteins. In: Journal of Structural Biology, 161 (1). pp. 31-42.

Kanade, Santosh R and Suhas, VL and Chandra, Nagasurna and Gowda, Lalitha R (2007) Functional interaction of diphenols with polyphenol oxidase - Molecular determinants of substrate/inhibitor specificity SO FEBS JOURNAL. In: FEBS Journal, 274 (16). pp. 4177-4187.

Kanaujia, SP and Jeyakanthan, J and Nakagawa, N and Balasubramaniam, S and Shinkai, A and Kuramitsu, S and Yokoyama, S and Sekar, K (2010) Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8. In: Acta Crystallographica Section D, 66 (Part 7). pp. 821-833.

Kanaujia, Shankar Prasad and Jeyakanthan, Jeyaraman and Shinkai, Akeo and Kuramitsu, Seiki and Yokoyama, Shigeyuki and Sekar, Kanagaraj (2011) Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms. In: Acta Crystallographica Section F, 67 (Part 1). pp. 2-16.

Kanaujia, Shankar Prasad and Ranjani, Chellamuthu Vasuki and Jeyakanthan, Jeyaraman and Baba, Seiki and Chen, Lirong and Liu, Zhi-Jie and Wang, Bi-Cheng and Nishida, Masami and Ebihara, Akio and Shinkai, Akeo and Kuramitsu, Seiki and Shiro, Yoshitsugu and Sekar, Kanagaraj and Yokoyama, Shigeyuki (2007) Crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein C from Thermus thermophilus. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 63 (Part 1). pp. 27-29.

Kanaujia, Shankar Prasad and Ranjani, Chellamuthu Vasuki and Jeyakanthan, Jeyaraman and Baba, Seiki and Kuroishi, Chizu and Ebihara, Akio and Shinkai, Akeo and Kuramitsu, Seiki and Shiro, Yoshitsugu and Sekar, Kanagaraj and Yokoyama, Shigeyuki (2007) Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communication, 63 (2). pp. 103-105.

Kanaujia, Shankar Prasad and Ranjani, Chellamuthu Vasuki and Jeyakanthan, Jeyaraman and Nishida, Masami and Kitamura, Yoshiaki and Baba, Seiki and Ebihara, Akio and Shimizu, Nobutaka and Nakagawa, Noriko and Shinkai, Akeo and Yamamoto, Masaki and Kuramitsu, Seiki and Shiro, Yoshitsugu and Sekar, Kanagaraj and Yokoyama, Shigeyuki (2007) Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 63 (5). pp. 446-448.

Kanaujia, Shankar Prasad and Ranjani, Chellamuthu Vasuki and Jeyakanthan, Jeyaraman and Ohmori, Miwa and Agari, Kazuko and Kitamura, Yoshiaki and Baba, Seiki and Ebihara, Akio and Shinkai, Akeo and Kuramitsu, Seiki and Shiro, Yoshitsugu and Sekar, Kanagaraj and Yokoyama, Shigeyuki (2007) Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of molybdopterin synthase from Thermus thermophilus HB8. In: Acta Crystallographica Section F-Structural Biology and Crystallization Communications, 63 (4). pp. 324-326.

Kant, Shashi and Bagaria, Ashima and Ramakumar, S (2002) Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity. In: Biochemical and Biophysical Research Communications, 299 (2). pp. 229-232.

Karthik, Raman and Rajagopalan, Preethi and Chandra, Nagasuma (2007) Hallmarks of mycolic acid biosynthesis: A comparative genomics study. In: Proteins: Structure, Function, and Bioinformatics, 69 (2). pp. 358-368.

Khodade, Prashant and Malhotra, Samta and Kumar, Nirmal and Iyengar, Sriram M and Balakrishnan, N and Chandra, Nagasuma (2007) Cytoview: Development of a cell modelling framework. In: Journal of Biosciences, 32 (5). pp. 965-977.

Khodade, Prashant and Prabhu, A and Chandra, Nagasuma and Raha, Soumyendu and Govindarajan, R (2007) Parallel implementation of AutoDock. In: Journal of Applied Crystallography, 40 (3). pp. 598-599.

Konkimalla, Badireenath V and Laxminarayana Suhas, Venkatramana and Chandra, Nagasuma R and Gebhart, Erich and Efferth, Thomas (2007) Diagnosis and therapy of oral squamous cell carcinoma. In: Expert Review of Anticancer Therapy, 7 (3). pp. 317-329.

Konkimalla, Badireenath V and Chandra, Nagasuma (2003) Determinants of histamine recognition: Implications for the design of antihistamines. In: Biochemical and Biophysical Research Communications, 309 (2). pp. 425-431.

Krishna, R and Manjunath, GP and Kumar, P and Surolia, A and Nagasuma, Chandra R and Muniyappa, K and Vijayan, M (2006) Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery. In: Nucleic Acids Research, 34 (9). 2186-2195.

Krishna, R and Prabu, Rajan J and Manjunath, GP and Datta, S and Chandra, NR and Muniyappa, K and Vijayan, M (2007) Snapshots of RecA Protein Involving Movement of the C-domain and Different Conformations of the DNA-binding Loops: Crystallographic and Comparative Analysis of 11 Structures of Mycobacterium smegmatis RecA. In: Journal of Molecular Biology, 367 (4). pp. 1130-1144.

Krishnan, Sheeja M and Dixit, Narendra M (2011) Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy. In: PLoS Computational Biology, 7 (2).

Kumar, Chetan and Sekar, K (2010) SSMBS: a web server to locate sequentially separated motifs in biological sequences. In: Journal of Applied Crystallography, 43 (Part 1). pp. 203-205.

Kumar, Pradeep and Rao, Appu AG and Hariharaputran, Sridhar and Chandra, Nagasuma and Gowda, Lalitha R (2004) Molecular Mechanism of Dimerization of Bowman-Birk Inhibitors: PIVOTAL ROLE OF $ASP^{76}$ IN THE DIMERZATION. In: The Journal of Biological Chemistry, 279 (29). pp. 30425-30432.

Kumari, Namita and Jha, Satadru and Bhattacharya, Santanu (2014) An Efficient Probe for Rapid Detection of Cyanide in Water at Parts per Billion Levels and Naked-Eye Detection of Endogenous Cyanide. In: CHEMISTRY-AN ASIAN JOURNAL, 9 (3). pp. 830-837.

Lahiri, Debojyoti and Bhowmick, Tuhin and Banik, Bhabatosh and Railkar, Reema and Ramakumar, Suryanarayanarao and Dighe, Rajan R and Chakravarty, Akhil R (2010) Photocytotoxic and anaerobic DNA cleavage activity of binuclear 3,3 '-dithiodipropionic acid cobalt(II) complexes having phenanthroline bases. In: Polyhedron, 29 (12). pp. 2417-2425.

Manikandan, K and Bhardwaj, Amit and Ghosh, Amit and Reddy, VS and Ramakumar, S (2005) Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 61 (Part 8). pp. 747-749.

Manikandan, K and Ramakumar, S (2004) The occurrence of C-H...O hydrogen bonds in alpha-helices and helix termini in globular proteins. In: Proteins: Structure, Function, and Genetics, 56 (4). pp. 768-781.

Manikandan, Karuppasamy and Pal, Debnath and Ramakumar, Suryanarayanarao and Brener, Nathan E and Iyengar, Sitharama S and Seetharaman, Guna (2008) Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. In: Genome Biology, 9 (3). R52.1-R52.18.

Manjunath, K and Jeyakanthan, J and Nakagawa, N and Shinkai, A and Yoshimura, M and Kuramitsu, S and Yokoyama, S and Sekar, K (2010) Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3. In: Acta Crystallographica Section F, 66 (Part 2). pp. 180-183.

Mathur, P and Ramagopal, UA and Ramakumar, Suryanarayanarao and Jagannathan, NR and Chauhan, VS (2006) Stabilization of unusual structures in peptides using alpha,beta-dehydrophenylalanine: Crystal and solution structures of Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe. In: Biopolymers, 84 (3). pp. 298-309.

Mathur, Puniti and Ramakumar, S and Chauhan, VS (2004) Peptide Design Using \alpha , \beta - Dehydro Amino Acids: From \beta -Turns to Helical Hairpins. In: Peptide Science, 76 (2). pp. 150-161.

Medrano-Soto, Arturo and Pal, Debnath and Eisenberg, David (2008) Inferring molecular function: contributions from functional linkages. In: Trends in Genetics, 24 (12). 587 -590.

Mitra, Anirban and Kesarwani, Anil K and Pal, Debnath and Nagaraja, Valakunja (2011) WebGeSTer DB-a transcription terminator database. In: Nucleic Acids Research, 39 (Suppl.). D129-D135.

Mitra, Pralay and Pal, Debnath (2011) Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference. In: Structure, 19 (3). pp. 304-312.

Mitra, Pralay and Pal, Debnath (2010) New measures for estimating surface complementarity and packing at protein-protein interfaces. In: FEBS Letters, 584 (6). pp. 1163-1168.

Mitra, Pralay and Pal, Debnath (2011) PRUNE and PROBE-two modular web services for protein-protein docking. In: Nucleic Acids Research, 39 (2). W229-W234.

Mitra, Pralay and Pal, Debnath (2011) Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys. In: Journal of Computational Chemistry, 32 (5). pp. 787-796.

Mitra, Pralay and Pal, Debnath (2011) DockYard-a repository to assist modeling of protein-protein docking. In: Journal of Molecular Modeling, 17 (3). pp. 599-606.

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Padyana, Anil K and Ramakumar, S (2006) Lateral energy transfer model for adjacent light-harvesting antennae rods of C-phycocyanins. In: Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1757 (3). pp. 161-165.

Parida, R and Shaila, MS and Mukherjee, S and Chandra, NR and Nayak, Rabindranath (2007) Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential. In: Vaccine, 25 (43). pp. 7530-7539.

Patra, Ashis K and Bhowmick, Tuhin and Ramakumar, Suryanarayanarao and Chakravarty, Akhil R (2007) Metal-Based Netropsin Mimics Showing AT-Selective DNA Binding and DNA Cleavage Activity at Red Light. In: Inorganic Chemistry:Communication, 46 (22). pp. 9030-9032.

Prabu, JR and Rangannan, V and Chandra, N (2006) Carbohydrate-based drug design: Recognition fingerprints and their use in lead identification. In: Indian Journal Of Chemistry Section A-Inorganic Bio-Inorganic Physical Theoretical & Analytical Chemistry, 45 (1). pp. 77-92.

Prabu, Rajan J and Manjunath, GP and Chandra, Nagasuma R and Muniyappa, K and Vijayan, M (2008) Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes. In: Acta Crystallographica Section D - Biological Crystallography, 64 (Part 1). pp. 1146-1157.

Prakash, Udaya NA and Jayanthi, M and Sabarinathan, R and Kangueane, P and Mathew, Lazar and Sekar, Kanagaraj (2010) Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases. In: Journal of Molecular Evolution, 70 (5). pp. 466-478.

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Pratap, JV and Jeyaprakash, Arockia A and Rani, Geetha P and Sekar, K and Surolia, A and Vijayan, M (2002) Crystal Structures of Artocarpin, a Moraceae Lectin with Mannose Specificity, and its Complex with Methyl-alpha-D-mannose: Implications to the Generation of Carbohydrate Specificity. In: Journal of Molecular Biology, 317 (2). pp. 237-247.

Praveen, S and Ramesh, J and Sivasankari, P and Sowmiya, G and Sekar, K (2008) WAP (version 2.0): an updated computing and visualization server for water molecules. In: Journal Of Applied Crystallography, 41 (Part 5). pp. 952-954.

Rajakannan, V and Govindasamy, L and Velmurugan, D and Sekar, K and Senthilvelan, A and Raj, Shanmuga Sundar S and Fun, HK (2002) The Crystal Structure of 4-(2-Chlorobenzyl)-5-phenyl-1,2,4-triazole. In: Crystal Research and Technology, 37 (2-3). pp. 301-308.

Ramachandraiah, Gosu and Chandra, Nagasuma R (2000) Sequence and Structural Determinants of Mannose Recognition. In: Proteins: Structure, Function, and Genetics, 39 (4). pp. 358-364.

Ramachandraiah, Gosu and Chandra, Nagasuma R and Surolia, A and Vijayan, M (2002) Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin. In: Acta Crystallographica Section D, 58 . pp. 414-420.

Ramagopal, Udupi A and Ramakumar, Suryanarayanarao and Mathur, Puniti and Joshi, Ratanmani and Chauhan, Virander S (2002) Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions. In: Protein Engineering, 15 (4). pp. 331-335.

Ramagopal, Udupi A and Ramakumar, Suryanarayanarao and Sahal, Dinkar and Chauhan, Virander S (2001) De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions. In: Proceedings of the National Academy of Sciences of the United States of America, 98 (3). 870-874.

Raman, K and Bhat, AG and Chandra, N (2010) A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. In: Molecular BioSystems, 6 (3). pp. 516-530.

Raman, K and Bhat, AG and Chandra, N (2010) A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. In: Molecular BioSystems, 6 (3). pp. 516-530.

Raman, Karthik and Chandra, Nagasuma (2009) Flux balance analysis of biological systems: applications and challenges. In: Briefings in bioinformatics, 10 (4). pp. 435-449.

Raman, Karthik and Rajagopalan, Preethi and Chandra, Nagasuma (2005) Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs. In: Public Library of Science Computational Biology, 1 (5). e46.

Raman, Karthik and Rajagopalan, Preethi and Chandra, Nagasuma (2006) Principles and Practices of Pathway Modelling. In: Current Bioinformatics, 1 (2). pp. 147-160.

Raman, Karthik and Vashisht, Rohit and Chandra, Nagasuma (2009) Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis. In: Molecular BioSystems, 5 (12). pp. 1740-1751.

Raman, Karthik and Yeturu, Kalidas and Chandra, Nagasuma R (2008) targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. In: BMC Systems Biology, 2 (109).

Ramesh, Sneha and Bharath, Srinivas MM and Chandra, Nagasuma R and Rao, Manchanahalli Satyanarayana R (2006) A K52Q substitution in the globular domain of histone H1t modulates its nucleosome binding properties. In: FEBS Letters, 580 (25). pp. 5999-6006.

Ramtekkar, Rahul and Kumarvel, Kandhasamy and Vasuki, Gnanasambandam and Sekar, K and Krishna, R (2009) Computer-Aided Drug Design of Pyranopyrazoles and Related Compounds for Checkpoint Kinase-1. In: Letters in Drug Design & Discovery, 6 (8). pp. 579-584.

Rangarajan, Sarani and Jeyakanthan, Jeyaraman and Palappetty, Mridula and Sakamoto, Keiko and Kitamura, Yoshiaki and Agari, Yoshihiro and Shinkai, Akeo and Ebihara, Akio and Kuramitsu, Seiki and Yokoyama, Shigeyuki and Sekar, Kanagaraj (2008) Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044). In: Acta Crystallographica Section F Structural Biology and Crystallization Communications, 64 . pp. 102-104.

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Raval, Sujana and Gowda, Sharan B and Singh, Desh D and Chandra, Nagasuma R (2004) A database analysis of jacalin-like lectins: Sequence-structure-function relationships. In: Glycobiology, 14 (12). pp. 1247-1263.

Raychaudhury, Chandan and Kandel, Durga D and Pal, Debnath (2014) Role of Vertex Index in Substructure Identification and Activity Prediction: A Study on Antitubercular Activity of a Series of Acid Alkyl Ester Derivatives. In: CROATICA CHEMICA ACTA, 87 (1). pp. 39-47.

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Raychaudhury, Chandan and Pal, Debnath (2012) Use of Vertex Index in Structure-Activity Analysis and Design of Molecules. In: CURRENT COMPUTER-AIDED DRUG DESIGN, 8 (2). pp. 128-134.

Roy, Mithun and Bhowmick, Tuhin and Ramakumar, Suryanarayanarao and Nethaji, Munirathinam and Chakravarty, Akhil R (2008) Double-strand DNA cleavage from photodecarboxylation of (\mu-oxo)diiron(III) L-histidine complex in visible light. In: Dalton Transactions (27). pp. 3542-3545.

Roy, Siddhartha and Gupta, Surbhi and Das, Satyabrata and Sekar, K and Chatterji, Dipankar and Vijayan, M (2004) X-ray Analysis of Mycobacterium smegmatis Dps and a Comparative Study Involving Other Dps and Dps-like Molecules. In: Journal of Molecular Biology, 339 (5). pp. 1103-1113.

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Roy, Siddhartha and Saraswathi, Ramachandran and Gupta, Surbhi and Sekar, K and Chatterji, Dipankar and Vijayan, M (2007) Role of N and C-terminal Tails in DNA Binding and Assembly in Dps: Structural Studies of Mycobacterium smegmatis Dps Deletion Mutants. In: Journal of Molecular Biology, 370 (4). pp. 752-767.

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Saikrishnan, K and Jeyakanthan, J and Venkatesh, J and Acharya, N and Purnapatre, K and Sekar, K and Varshney, U and Vijayan, M (2002) Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis. In: Acta Crystallographica Section D, 58 . pp. 327-329.

Saikrishnan, K and Jeyakanthan, J and Venkatesh, J and Acharya, N and Sekar, K and Varshney, U and Vijayan, M (2003) Structure of Mycobacterium tuberculosis Singlestranded DNA-binding Protein. Variability in Quaternary Structure and Its Implications. In: Journal of Molecular Biology, 331 (2). pp. 385-393.

Saikrishnan, K and Manjunath, GP and Singh, Pawan and Jeyakanthan, J and Dauter, Z and Sekar, K and Muniyappa, K and Vijayan, M (2005) Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association. In: Acta Crystallographica Section D: Biological Crystallography, 61 . pp. 1140-1148.

Sarani, R and Udayaprakash, NA and Subashini, R and Mridula, P and Yamane, T and Sekar, K (2009) Large cryptic internal sequence repeats in protein structures from Homo sapiens. In: Journal Of Biosciences, 34 (1). pp. 103-112.

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Sekar, K and Yogavel, M and Kanaujia, ShankarPrasad and Sharma, Alok and Velmurugan, D and Poi, MJ and Dauter, Z and Tsai, MD (2006) Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2. In: Acta Crystallographica Section D-Biological Crystallography, 62 (7). pp. 717-724.

Selvarani, P and Shanthi, V and Rajesh, CK and Saravanan, S and Sekar, K (2004) BSDD: Biomolecules Segment Display Device—a web-based interactive display tool. In: Nucleic Acids Research, 32 . W645-W648.

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Sheik, SS and Aggarwal, Sumit K and Poddar, A and Sathiyabhama, B and Balakrishna, N and Sekar, K (2005) Analysis of string-searching algorithms on biological sequence databases. In: Current Science, 89 (2). pp. 368-374.

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Sheik, SS and Sundararajan, P and Shanthi, V and Sekar, K (2003) CAP: conformation angles package—displaying the conformation angles of side chains in proteins. In: Bioinformatics, 19 (8). pp. 1043-1044.

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Shobini, J and Mishra, AK and Sandhya, K and Chandra, Nagasuma (2001) Interaction of coumarin derivatives with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studies. In: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 57 (5). pp. 1133-1147.

Singh, Desh Deepak and Chandran, Divya and Jeyakani, Justin and Chandra, Nagasuma (2007) Scanning the genome of Mycobacterium tuberculosis to identify potential lectins. In: Protein and Peptide Letters, 14 (7). pp. 683-691.

Singh, DD and Saikrishnan, K and Kumar, Prashant and Dauter, Z and Sekar, K and Surolia, A and Vijayan, M (2004) Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca. In: Acta Crystallographica Section D: Biological Crystallography, 60 (11). pp. 2104-2106.

Singh, DD and Saikrishnan, K and Kumar, Prashant and Surolia, A and Sekar, K and Vijayan, M (2005) Unusual sugar specificity of banana lectin from Musa paradisiaca andits probable evolutionary origin. Crystallographic and modelling studies. In: Glycobiology, 15 (10). pp. 1025-1032.

Sivakumar, S and Franco, OL and Thayumanavan, B and Murad, AM and Manickam, A and Mohan, A and Mridula, M (2006) Cloning and Structural Analysis of an Indian Little Millet (Panicum sumatrense) Zein-Like Storage Protein: Implications for Molecular Assembly. In: Biochemistry(Moscow), 71 (11). pp. 1183-1191.

Sridhar, Jayavel and Narmada, Suryanarayanan Ramkumar and Sabarinathan, Radhakrishnan and Ou, Hong-Yu and Deng, Zixin and Sekar, Kanagaraj and Rafi, Ziauddin Ahamed and Rajakumar, Kumar (2010) sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes. In: PLos One, 5 (8).

Tejasvini, Prasad and Tamilselvi, Subramanian and Sridhar, Hariharaputran and Chaitra, HS and Nagasuma, Chandra (2004) Extracting Hydrogen-Bond Signature Patterns from Protein Structure Data. In: Applied Bioinformatics, 3 (2-3). pp. 125-135.

Thathoo, Rahul and Virmani, Ashish and Lakshmi, Sai S and Balakrishnan, N and Sekar, K (2006) TVSBS: A fast exact pattern matching algorithm for biological sequences. In: Current Science, 91 (1). pp. 47-53.

Uthayakumar, Muthukumarasamy and Patra, Sanjeev and Nagarajan, Raju and Sekar, Kanagaraj (2012) Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures? In: Current Bioinformatics, 7 (2). pp. 111-115.

Uthayakumar, Muthukumarasamy and Sowmiya, Govindhan and Sabarinathan, Radhakrishnan and Udayaprakash, N and Vaishnavi, Kirti M and Sekar, Kanagaraj (2011) BSSB: BLAST Server for Structural Biologists. In: Journal of Applied Crystallography, 44 (Part 3). pp. 651-654.

Vani, J and Chatterjee, Jhinuk and Shaila, MS and Nayak, R and Chandra, NR (2009) Structural basis for the function of anti-idiotypic antibody in immune memory. In: Molecular Immunology, 46 (6). pp. 1250-1255.

Vani, J and Chatterjee, Jhinuk and Shaila, MS and Nayak, R and Chandra, Nagasuma R (2009) Structural basis for the function of anti-idiotypic antibody in immune memory. In: Molecular Immunology, 46 (6). pp. 1250-1255.

Vani, J and Justin, Jayakani and Nagasuma, Chandra R and Nayak, Rabindranath and Shaila, MS (2007) Peptidomimics of antigen are present in variable region of heavy and light chains of anti-idiotypic antibody and function as surrgate antigen for perpetuation of immunological memory. In: Molecular Immunology, 44 (13). pp. 3345-3354.

Vasu, * and Nirmala, KA and Choudhury, AR and Mohan, S and Saravanan, J and Narasimhamurthy, T (2003) Two biologically active thiophene-3-carboxamide derivatives. In: Acta Crystallographica Section C: Crystal Structure Communications, 59 (12). o676-o678.

Verkhedkar, K and Raman, K and Chandra, Nagasuma R and Vishveshwara, Saraswathi (2007) Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis. In: PLOS ONE, 2 (9).

Vijayan, M and Chandra, Nagasuma (1999) Lectins. In: Current Opinion in Structural Biology, 9 (6). pp. 707-714.

Yathirajan, HS and Narasimhamurthy, T and Nagaraj, B and Nagaraja, P and Narasegowda, RS and Rathore, Ravindranath S (2005) $N-H^+{\cdot\cdot\cdot}Cl^-\hspace{5 mm}and\hspace {5 mm}C-H{\cdot\cdot\cdot}O$ interactions in 6-fluoro-3-(4-piperidinio)benz[d]isoxazole chloride. In: Acta Crystallographica Section E: Structure Reports Online, 61 (2). o356-o358.

Yeturu, Kalidas and Chandra, Nagasuma (2011) PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures. In: Journal of Chemical Information and Modeling, 51 (7). pp. 1725-1736.

Yeturu, Kalidas and Chandra, Nagasuma (2008) PocketMatch: A new algorithm to compare binding sites in protein structures. In: BMC Bioinformatics, 9 . pp. 543-560.

Yeturu, Kalidas and Utriainen, Tapani and Kemp, Graham JL and Chandra, Nagasuma (2010) An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. In: BMC Bioinformatics, 11 (Suppl.).

Yeturu, Kalidas and Utriainen, Tapani and Kemp, Graham JL and Chandra, Nagasuma (2010) An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. In: BMC Bioinformatics, 11 (Suppl.).

Yogavel, M and Velmurugan, D and Sekar, K and Schenk, H and Fraanje, J and Peschar, R and Srinivasan, S and Athappan, PR and Rafi, ZA (2003) 3-Acetyl-2-hydroxy-2-methylchromene. In: Acta Crystallographica Section E, 59 (5). 0591-0593.

Editorials/Short Communications

Krishnan, Sheeja M and Dixit, Narendra (2010) Mathematical model of Ribavirin-Induced Anemia In Hepatitis C Virus(HCV) Patients undergoing combination therapy estimates Optimal Ribavirin Exposure and Suggests Guidelines for the Use of Hormone (ERYTHROPOIETIN) Supplements. In: Hepatology, 52 (4, Sup). p. 935.

Sambarey, Awanti and Chandra, Nagasuma (2010) Structural profiles of cytokine families - Revisiting classification. In: Cytokine, 52 (1-2, S). p. 87.

This list was generated on Tue Oct 21 18:41:41 2014 IST.