Roy, Siddhartha, Saraswathi, Ramachandran, Gupta, Surbhi, Sekar, K, Chatterji, Dipankar, Vijayan, M
Mycobacterium smegmatis Dps degrades spontaneously into a species in which 16 C-terminal residues are cleaved away. A second species, in which all 26 residues constituting the tail were deleted, was...
PSAP: protein structure analysis package (2007)
Balamurugan, B, Roshan, Md MNA, Hameed, Shaahul B, Sumathi, K, Senthilkumar, R, Udayakumar, A, ...
A computing engine, the Protein Structure Analysis Package (PSAP), has been developed to calculate and display various hidden structural and functional features of three-dimensional protein...
Ramachandran Plot on The Web (2.0) (2007)
Gopalakrishnan, K, Sowmiya, G, Sheik, SS, Sekar, K
The Ramachandran plot displays the main chain conformation angles (\Phi and \Psi) of the polypeptide chain of a protein molecule. The paper reports the updated version of the Ramachandran plot web...
Sekar, K, Yogavel, M, Gayathri, D, Velmurugan, D, Krishna, R, Poi, MJ, ...
The structure of the double mutant K53,56M has previously been refined at 1.9 A resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M...
TVSBS: A fast exact pattern matching algorithm for biological sequences (2006)
Thathoo, Rahul, Virmani, Ashish, Lakshmi, Sai S, Balakrishnan, N, Sekar, K
The post-genomic era is witnessing a remarkable increase in the number of nucleotide and amino acid sequences. The content of biological sequence databases almost doubles frequently. Pattern matching...
3dSS: 3D structural superposition (2006)
Sumathi, K, Ananthalakshmi, P, Sekar, K
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the...
SSEP-2.0: Secondary Structural Elements of Proteins (2005)
Balamurugan, B, Mohan, Samaya K, Ramesh, J, Roshan, Md MNA, Sumathi, K, Sekar, K
The Secondary Structural Elements of Proteins (SSEP) database is an integrated and comprehensive knowledge base for accessing information related to all the secondary-structural elements present in...
CADB-2.0: Conformation Angles Database (2005)
Mohan, Samaya K, Sheik, SS, Ramesh, J, Balamurugan, B, Jeyasimhan, M, Mayilarasi, C, ...
The Conformation Angles Data Base (CADB) is a comprehensive,authoritative and timely knowledge base with a powerful query engine developed to facilitate the retrieval of information related to the...
Fragment Finder: A Web-based Software to Identify Similar three-dimensional Structural Motif (2005)
Ananthalakshmi, P, Kumar, Kiran M, Jeyasimhan, M, Sumathi, K, Sekar, K
FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the userdesired similar 3D structural fragments from the selected subset of 25 or90%non-homologous protein chains....
Saikrishnan, K, Manjunath, GP, Singh, Pawan, Jeyakanthan, J, Dauter, Z, Sekar, K, ...
The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its...
Singh, DD, Saikrishnan, K, Kumar, Prashant, Surolia, A, Sekar, K, Vijayan, M
The crystal structure of a complex of methyl-\alpha-D-mannoside with banana lectin from Musa paradisiaca reveals two primary binding sites in the lectin, unlike in other lectins with beta-prism I...
Sekar, K, Rajakannan, V, Gayathri, D, Velmurugan, D, Poi, MJ, Dauter, M, ...
The enzyme phospholipase $A_{2}$ catalyzes the hydrolysis of the sn-2 acyl chain of phospholipids, forming fatty acids and lysophospholipids. The crystal structure of a triple mutant (K53,56,121M) of...
Jeyaprakash, Arockia A, Jayashree, G, Mahanta, SK, Swaminathan, CP, Sekar, K, Surolia, A, ...
Jacalin, a tetrameric lectin, is one of the two lectins present in jackfruit (Artocarpus integrifolia) seeds. Its crystal structure revealed, for the first time, the occurrence of the $\beta$-prism I...
Analysis of string-searching algorithms on biological sequence databases (2005)
Sheik, SS, Aggarwal, Sumit K, Poddar, A, Sathiyabhama, B, Balakrishna, N, Sekar, K
String-searching algorithms are used to find the occurrences of a search string in a given text. The advent of digital computers has stimulated the development of string-searching algorithms for...
Sekar, K, Rajakannan, V, Velmurugan, D, Yamane, T, Thirumurugan, R, Dauter, M, ...
The crystal structure of the triple mutant K53,56,120M of bovine pancreatic phospholipase A(2) has been redetermined using sulfur single-wavelength anomalous scattering. The synchrotron data-were...
A FAST Pattern Matching Algorithm (2004)
Sheik, SS, Aggarwal, Sumit K, Poddar, Anindya, Balakrishnan, N, Sekar, K
The advent of digital computers has made the routine use of pattern-matching possible in various applications.This has also stimulated the development of many algorithms. In this paper, we propose a...
Singh, DD, Saikrishnan, K, Kumar, Prashant, Dauter, Z, Sekar, K, Surolia, A, ...
The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been...
Roy, Siddhartha, Gupta, Surbhi, Das, Satyabrata, Sekar, K, Chatterji, Dipankar, Vijayan, M
The structure of the DNA binding protein from starved cells from Mycobacterium smegmatis has been determined in three crystal forms and has been compared with those of similar proteins from other...
LySDB - Lysozyme Structural DataBase (2004)
Mohan, Samaya K, Das, Soma, Chockalingam, C, Shanthi, V, Sekar, K
LySDB (Lysozyme Structural DataBase) is an integrated database containing 740 three-dimensional structures of lysozyme available in the Protein Data Bank. The database can be used to visualize the...
Muktha, B, Srinivas, O, Amresh, MR, Row, Guru TN, Jayaraman, N, Sekar, K
In the above article, the ORTEP diagram and the associated torsion angles are those of the L-isomer, rather than those of the D-isomer of the title compound.
THGS:a web-based database of Transmembrane Helices in Genome Sequences (2004)
Fernando, SA, Selvarani, P, Das, Soma, Kumar, Kiran Ch, Mondal, Sukanta, Ramakumar, S, ...
Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome...
Muktha, B, Srinivas, O, Amresh, MR, Row, Guru TN, Jayaraman, N, Sekar, K
The crystal structure of the title compound was determined by X-ray crystallography. The compound crystallized in the orthorhombic space group $P2_12_12_1$ with four molecules in the unit cell with...
K. Sekar, P. C. Srinivasan, S. Shanmuga, Sundara Raj, Bioinformatics Centre, Key Indicators
e solid state is stabilized by CHO, CH and intermolecular interactions. Comment The indole ring system is present in a number of natural products, many of which are found to possess antibacterial...
Saikrishnan, K, Jeyakanthan, J, Venkatesh, J, Acharya, N, Sekar, K, Varshney, U, ...
Single-stranded DNA-binding protein (SSB) is an essential protein necessary for the functioning of the DNA replication, repair and recombination machineries. Here we report the structure of the...
Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study (2003)
Jeyaprakash, Arockia A, Katiyar, S, Swaminathan, CP, Sekar, K, Surolia, A, Vijayan, M
The structures of the complexes of tetrameric jacalin with Gal, Me-a-Gal-NAc, Me-a-T-antigen, GalNAcb1-3Gal-a-O-Me and Gala1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three...
Crystallization and preliminary X-ray diffraction analysis of Mycobacterium smegmatis Dps (2003)
Roy, Siddhartha, Gupta, Surbhi, Das, Surbhi, Sekar, K, Chatterji, Dipankar, Vijayan, M
Three crystal forms of a DNA-binding protein from stationary phase cells (Dps) of Mycobacterium smegmatis have been grown. They are hexagonal, tetragonal and cubic. The structure of the cubic form,...
Crystal and molecular structure of 2,6-bis(4-chlorophenyl)-3-phenylpiperidin-4-one (2003)
Ompraba, G, Srinivasan, M, Perumal, S, Sekar, K, Choudhury, AR, Row, Guru TN, ...
The crystal structure of the title compound is described. The chemical formula of the compound is $C_2_3H_1_9C_l_2NO$. The compound is found to crystallize in monoclinic system with space group...
Crystal and molecular structure of 2,6-bis(4 fluorobenzylidene)cyclohexanone (2003)
Ompraba, G, Rafi, ZA, Yogavel, M, Velmurugan, D, Sekar, K, Karthikeyan, E, ...
The title compound, $C_20H_1_6F_2O$, crystallizes in triclinic system with P1 space group and the unit cell parameters are: a = 9.700(5), b = 11.834(6), c = 14.315(7) $A^o$, \alpha = 78.464(9), \beta...
C–halogen…\pi interactions in proteins: a database study (2003)
Saraogi, Ishu, Vijay, VG, Das, Soma, Sekar, K, Row, Guru TN
A Protein Data Bank (PDB) study was undertaken to investigate the role of C–X…\pi interactions (X = F, Cl, Br, I) in protein structures. From this analysis, it is evident that the propensity for...
Side-chain conformation angles of amino acids: effect of temperature factor cut-off (2003)
Bhargavi, Ramya G, Sheik, SS, Velmurugan, D, Sekar, K
The paper presents the analysis of the side-chain conformation angles of amino acids in 90% non-identical protein structures. The analysis has been carried out using 113,699 residues, which is higher...
Crystal Structures of the Free and Anisic Acid Bound Triple Mutant of Phospholipase $A_2$ (2003)
Sekar, K, Mala, Vaijayanthi S, Yogavel, M, Velmurugan, D, Poi, Ming-Jye, Vishwanath, BS, ...
Phospholipase $A_2$ catalyses the hydrolysis of the ester bond of 3-sn-phosphoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of...
3-benzoyl-2-hydroxy-2-methylchromene. (2003)
Yogavel, M., Velmurugan, D., Sekar, K., Schenk, H., Fraanje, J., Peschar, R., ...
3-Acetyl-2-hydroxy-2-methylchromene (2003)
Yogavel, M., Velmurugan, D., Sekar, K., Schenk, H., Fraanje, J., Peschar, R., ...
Shanthi, V, Rajesh, CK, Jayalakshmi, J, Vijay, VG, Sekar, K
With the advent of Internet computing and World Wide Web technology, Web browsers have provided powerful tools for server and client-side applications. Exploiting this rapidly growing technology, the...
CADB: Conformation Angles DataBase of proteins (2003)
Sheik, S S, Ananthalakshmi, P, Bhargavi, G R, Sekar, K
Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and...
Hussain, ASZ, Kumar, Kiran Ch, Rajesh, CK, Sheik, SS, Sekar, K
SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows...
SSEP: Secondary structural elements of proteins (2003)
Shanthi, V, Selvarani, P, Kumar, Kiran Ch, Mohire, CS, Sekar, K
SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein...
Muktha, B, Srinivas, O, Amresh, MR, Row, TNG, Jayaraman, N, Sekar, K
The crystal structure of the title compound was determined by X-ray crystallography. The compound crystallized in the orthorhombic space group $P2_12_12_1$ with four molecules in the unit cell with...
Saikrishnan, K, Jeyakanthan, J, Venkatesh, J, Acharya, N, Purnapatre, K, Sekar, K, ...
Single-stranded DNA-binding proteins play an important role in DNA replication, repair and recombination. The protein from Mycobacterium tuberculosis (MtSSB) is a tetramer with 164 aminoacid residues...
Pratap, JV, Jeyaprakash, Arockia A, Rani, Geetha P, Sekar, K, Surolia, A, Vijayan, M
The seeds of jack fruit (Artocarpus integrifolia) contain two tetrameric lectins, jacalin and artocarpin. Jacalin was the first lectin found to exhibit the b-prism I fold, which is characteristic of...
Jeyaprakash, Arockia A, Rani, Geetha P, Reddy, Banuprakash G, Banumathi, S, Betzel, C, Sekar, K, ...
Thomsen–Friedenreich antigen (Galbeta1–3GalNAc), generally known as T-antigen, is expressed in more than 85% of human carcinomas. Therefore, proteins which specifically bind T-antigen have...
Crystal and Molecular Structure of an Acridinedione (2002)
Jeyakanthan, J, Yogavel, M, Rajan, Joseph T, Velmurugan, D, Sekar, K
The title compound, 10-(4-hydroxybenzoylamino)-3,4,6,7,9,10-hexahydro-1,8-(2H,5H)-acridinedione monohydrate, $C_20H_2_2N_2O_4.H_2O$, consists of partially hydrogenated acridine moiety with one...
The Crystal Structure of 4-(2-Chlorobenzyl)-5-phenyl-1,2,4-triazole (2002)
Rajakannan, V, Govindasamy, L, Velmurugan, D, Sekar, K, Senthilvelan, A, Raj, Shanmuga Sundar S, ...
The crystal structure of the title compound [CCDC No. 157498], $C_1_5H_1_2N_3Cl$, contains a 1,2,4-triazole moiety substituted with a phenyl ring and methyl chlorophenyl group as exogenous...
Protein sequence search tool:A web-based interactive search engine (2000)
Saravanan, S, Khan, Ajmal A, Sekar, K
Protein sequence search tool (PSST) is a web-based interactive search tool developed to extract and analyse the protein/nucleic acid sequence and other related information from the database of...
Crystal and Molecular Structure of Desmodin (2000)
Ajees, Abdul A, Sekar, K, Parthasarathy, S, Balakrishna, K
The crystal structure of the title compound has been determined from X-ray diffraction. The compound crystallizes from benzene in the orthorhombic system, space group P212121, with unit cell...
Natesh, R, Bhanumoorthy, P, Vithayathil, PJ, Sekar, K, Ramakumar, S, Viswamitra, MA
Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component in the biosphere. Crystals belonging to $P2_1$space group with a = 41.7 \AA, b = 68.1...
Shape Transition in the Epitaxial Growth of Gold Silicide in Au Thin Films on Si(111) (1994)
Sekar, K., Kuri, G., Satyam, P. V., Sundaravel, B., Mahapatra, D. P., Dev, B. N.
Growth of epitaxial gold silicide islands on bromine-passivated Si(111) substrates has been studied by optical and electron microscopy, electron probe micro analysis and helium ion backscattering....
Chen, X, Mitra, S N, Rao, S T, Sekar, K, Sundaralingam, M
Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and...
CADB: Conformation Angles DataBase of proteins
Sheik, S. S., Ananthalakshmi, P., Bhargavi, G. Ramya, Sekar, K.
Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and...
SSEP: secondary structural elements of proteins
Shanthi, V., Selvarani, P., Kiran Kumar, Ch., Mohire, C. S., Sekar, K.
SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein...
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
Hussain, A. S. Z., Kumar, Ch. Kiran, Rajesh, C. K., Sheik, S. S., Sekar, K.
SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows...
THGS: a web-based database of Transmembrane Helices in Genome Sequences
Fernando, S. A., Selvarani, P., Das, Soma, Kumar, Ch. Kiran, Mondal, Sukanta, Ramakumar, S., ...
Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome...
BSDD: Biomolecules Segment Display Device—a web-based interactive display tool
Selvarani, P., Shanthi, V., Rajesh, C. K., Saravanan, S., Sekar, K.
An interactive web-based display tool, Biomolecules Segment Display Device (BSDD), has been developed to search for and visualize a user-defined motif or fragment among the protein structures...
Fragment Finder: a web-based software to identify similar three-dimensional structural motif
Ananthalakshmi, P., Kumar, Ch. Kiran, Jeyasimhan, M., Sumathi, K., Sekar, K.
FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein...
3dSS: 3D structural superposition
Sumathi, K., Ananthalakshmi, P., Sekar, K.
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the...
Chen, X, Mitra, S N, Rao, S T, Sekar, K, Sundaralingam, M
Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and...
CADB: Conformation Angles DataBase of proteins
Sheik, S. S., Ananthalakshmi, P., Bhargavi, G. Ramya, Sekar, K.
Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and...
SSEP: secondary structural elements of proteins
Shanthi, V., Selvarani, P., Kiran Kumar, Ch., Mohire, C. S., Sekar, K.
SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein...
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
Hussain, A. S. Z., Kumar, Ch. Kiran, Rajesh, C. K., Sheik, S. S., Sekar, K.
SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows...