In-house developed internet computing servers

Contact Person : Professor K. Sekar

  • PSST: Protein Sequence Search Tool - A web based interactive search engine
    S. Saravanan, A. Ajmal Khan and K. Sekar
    CURR. SCIENCE. (2000), 550-552.
    and
    PSST(2.0): PDB Sequence Search Tool - A web based interactive search engine
    P.Ananthalakshmi, K.Samaya Mohan, C.Chockalingam, C.Mayilarasi and K. Sekar
    APPL. BIOINFO. (2005).4(2), 141-145.  
    http://pranag.physics.iisc.ac.in/psst/

  • PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file
    A.S.Z. Hussain, V. Shanthi, S.S. Sheik, J. Jeyakanthan, P. Selvarani and K. Sekar
    ACTA CRYST. (2002), D58, 1385-1386  
    http://dicsoft2.physics.iisc.ac.in/pdbgoodies/

  • RP: Ramachandran plot on the web
    S.S. Sheik, P. Sundararajan, A.S.Z. Hussain and K. Sekar
    BIONFORMATICS (2002), 18, 1548-1549.
    and
    RP(2.0): Ramachandran plot on the web
    K. Gopalakrishnan, G. Sowmiya, S.S. Sheik and K. Sekar
    PROTEIN PEPT. LETT. (2007), 14, 669-671.  
    http://dicsoft1.physics.iisc.ac.in/rp/

  • WAP: Water Analysis Package - a Web-based package to calculate geometrical parameters between water oxygen and protein atoms
    V. Shanthi, C.K. Rajesh, J. Jayalakshmi, V.G. Vijay and K. Sekar
    J. APPL. CRYST. (2003), 36, 167-168.
    http://dicsoft2.physics.iisc.ac.in/wap/

  • CAP: Conformation Angles Package - Displaying the conformation angles of side chains in proteins
    S.S. Sheik, P. Sundararajan, V. Shanthi and K. Sekar
    BIOINFORMATICS. (2003), 19, 1043-1044.  
    http://dicsoft1.physics.iisc.ac.in/cap/

  • SEM : Symmetry Equivalent Molecules - A web based GUI to generate and visualize the macromolecules
    A.S.Z. Hussain, Ch.Kiran Kumar, C.K. Rajesh, S.S.Sheik and K. Sekar
    NUCL. ACIDS RES. (2003), 31, 3356-3358.  
    http://dicsoft2.physics.iisc.ac.in/sem/

  • BSDD: Biomolecules Segment Display Device - A web based interactive display tool
    P. Selvarani, V. Shanthi, C.K. Rajesh, S. Saravanan and K. Sekar
    NUCL. ACIDS RES. (2004), 32, W645-W648.  
    and
    BSDD(2.0): Biomolecules Segment Display Device
    Sanjeev Kumar, S.Praveen, R.Karthi, R.Sabarinathan, M.Kalaivani, S.Sathiyamoorthy and K. Sekar
    CURR. SCIENCE (2009). 97, 28-32.
    http://iris.physics.iisc.ac.in/bsdd/

  • FF : Fragment Finder - A web based software to identify similar three-dimensional structural motif
    P. Ananthalakshmi, Ch. Kirankumar, M. Jeyasimhan, K. Sumathi and K. Sekar
    NUCL ACIDS RES. (2005), 33, W85-W88.  
    and
    Fragment Finder 2.0: A computing server to identify structurally similar fragments
    R. Nagarajan, S. Siva Balan, R. Sabarinathan, M. Kirti Vaishnavi and K. Sekar
    J. APPL. CRYST. (2012). 45, 332-334.
    http://cluster.physics.iisc.ac.in/ff/

  • 3dSS: 3-Dimensional Structural Superposition
    K.Sumathi, P. Ananthalakshmi, M.N.A.Md.Roshan and K. Sekar
    NUCL. ACIDS RES. (2006). 34, W128-W134.  
    http://cluster.physics.iisc.ac.in/3dss/

  • PSAP: Protein Structure Analysis Package
    B.Balamurugan, M.N.A.Md.Roshan, B.Shaahul Hameed, K.Sumathi, R.Senthil Kumar, A.Udayakumar, K.H.Venkatesh Babu, M.Kalaivani, G.Sowmiya, P.Sivasankari, S.Saravanan, C.Vasuki Ranjani, K.Gopalakrishnan, K.N.Selvakumar, M.Jaikumar, T.Brindha, Daliah Michael and K. Sekar
    J. APPL. CRYST. (2007). 40, 773-777.
    http://iris.physics.iisc.ac.in/psap/

  • RPMS : Ramachandran Plot for Multiple Structures
    K.Gopalakrishnan, S. Saravanan, R. Sarani and K. Sekar
    J. APPL. CRYST. (2008). 41, 219-221.
    http://cluster.physics.iisc.ac.in/rpms/

  • CSSP : Consensus Secondary Structure Prediction
    Ankit Gupta, Avnish Deshpande, Janardhan Kumar Amburi, Radhakrishnan Sabarinathan, Ramaswamy Senthilkumar and K. Sekar
    J. APPL. CRYST. (2009) 42, 336-338.
    http://bioserver1.physics.iisc.ac.in/cssp/
    • and
    CSSP-2.0: A refined Consensus method for accurate protein secondary structure prediction
    Madhumathi Sanjeevi, Ajitha Mohan, Dhanalakshmi Ramachandran, Jeyakanthan Jeyaraman and K. Sekar
    Computational Biology and Chemistry (2024).  Vol 112, No.108158   doi: 10.1016/j.compbiolchem.2024.108158.
    http://bioserver3.physics.iisc.ac.in/cgi-bin/cssp-2/

  • FAIR: A Server for Internal Sequence Repeats
    R. Senthilkumar, R. Sabarinathan, B. Shaahul Hameed, Nirjhar Banerjee, N.Chidambarathanu, R. Karthi and K. Sekar
    BIOINFORMATION (2010). 4(7), 271-275.  
    http://bioserver1.physics.iisc.ac.in/fair/

  • ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures
    R. Sabarinathan, Raunak Basu and K. Sekar
    COMPUT. BIO. CHEM. (2010). 34(2), 126-130.  
    http://cluster.physics.iisc.ac.in/prostrip/

  • BSSB: Blast Server for Structural Biologists
    M. Uthayakumar, G. Sowmiya, R. Sabarinathan, N.A. Udaya Prakash, M. Kirti Vaishnavi and K. Sekar
    J. APPL. CRYST. (2011). 44, 651-654.
    http://bioserver1.physics.iisc.ac.in/bssb/

  • RPS: Repeats in Protein Sequences
    K.H. Venkatesh, M. Uthayakumar, M. Kirti Vaishnavi, R. Senthilkumar, M. Shankar, C. Archana, S. Sathya Priya and K. Sekar
    J. APPL. CRYST. (2011). 44, 647-650.
    http://bioserver1.physics.iisc.ac.in/rps/

  • Junker: An Intergenic Explorer for Bacterial genomes
    Jayavel Sridhar, Radhakrishnan Sabarinathan, Shanmugam Siva Balan, Ziauddin Ahamed Rafi, Paramasamy Gunasekaran and K. Sekar
    GENOMICS, PROTEOMICS AND BIOINFORMATICS (2011). 9(4-5), 179-182.   
    http://pranag.physics.iisc.ac.in/junker/

  • RepEx: Repeat Extractor for Biological Sequences.
    M. Gurusaran, Dheeraj Ravella and K. Sekar
    GENOMICS (2013), 102(4), 403-408.   
    http://pranag.physics.iisc.ac.in/RepEx

  • PPS: A computing engine to find Palindromes in all Protein sequences.
    Z. Zameer Ahmed, M. Gurusaran, Prasanth Narayanan, K. S. Dinesh Kumar, J. Mohanapriya, M. Kirti Vaishnavi and K. Sekar
    BIOINFORMATION (2014). 10(1), 48-51.  
    http://pranag.physics.iisc.ac.in/pps

  • Online_DPI: A web server to Calculate the Diffraction Precision Index for a Protein Structure.
    K. S. Dinesh Kumar, M. Gurusaran, S. N. Satheesh, P. Radha, S. Pavithra, K. P. S. Thulaa Tharshan, John R. Helliwell and K. Sekar
    J. APPL. CRYST (2015). 48, 939-942.
    http://cluster.physics.iisc.ac.in/dpi

  • Hydrogen Bond Computing Server (HBCS): An online web server to compute hydrogen bond interactions with its precision.
    M. Gurusaran, P. Sivaranjan, K.S. Dinesh Kumar, P. Radha, K.P.S. Thulaa Tharshan, S.N. Satheesh, K. Jayanthan, R. Ilaiyaraja, J. Mohanapriya and K. Sekar
    J. APPL. CRYST (2016) Vol 49, 642-645.
    http://bioserver1.physics.iisc.ac.in/hbcs

  • PanGeT: Pan-Genomics Tool.
    Iyyappan Yuvaraj, Jayavel Sridhar, Daliah Michael and K. Sekar
    GENE. 2017 Feb 5;600:77-84. doi: 10.1016/j.gene.2016.11.025.  
    http://pranag.physics.iisc.ac.in/PanGeT/

  • Glaucoma Pred: Glaucoma prediction based on Myocilin genotype and phenotype information
    K. Rangachari, Namrata Bankoti, N. Shyamala, Daliah Michael, Z. Sameer Ahmed, P. Chandrasekaran and K. Sekar
    Genomics(2018)30087-9. doi: 10.1016/j.ygeno.2018.04.006.   
    http://bioserver1.physics.iisc.ac.in/myocilin/index.php

  • PlaneFinder: A methodology to find the best plane for a set of atoms involved in the metal coordination in the protein structures
    Janu Sahana J, Sriraghav Srinivasan, Vijeth T A, Nagarushyanth Tummala, Santhosh Rajendran, Daliah Michael, Sameer Ahmed Z, Nisha K P R, Jeyakanthan Jeyaraman and K. Sekar
    Journal of Applied Crystallography (2018), Vol 51, 1251-1256.doi:10.1107/S1600576718008282.
    http://bioserver1.physics.iisc.ac.in/plane/

  • RepEx: A web server to extract sequence repeats from Protein and DNA sequences
    Daliah Michael, Gurusaran Manickam, Santhosh Rajendran, Md. Khaja Hussain, Satheesh S. N, Suhan S, Sivaranjan P, Akanksha Jaiswal and K. Sekar
    Computational Biology and Chemistry (2019),Vol 78, 424-430. doi:10.1016/j.compbiolchem.2018.12.015.  
    http://bioserver2.physics.iisc.ac.in/RepEx/