• 5410 Citations
  • 37 h-Index
1980 …2021

Research output per year

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Research Outputs

Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage

Choo, K. H., Tong, J. C. & Ranganathan, S., 13 Feb 2008, In : BMC Bioinformatics. 9, SUPPL. 1, p. 1-7 7 p., S15.

Research output: Contribution to journalArticle

Open Access
File
11 Citations (Scopus)
2 Downloads (Pure)

Modeling the bound conformation of Permphigus Vulgaris-associated peptides to MHC Class II DR and DQ Alleles

Tong, J. C., Bramson, J., Kanduc, D., Chow, S., Sinha, A. A. & Ranganathan, S., 2006, In : Immunome Research. 2, 1, 10 p.

Research output: Contribution to journalArticle

Open Access
File

Modeling the structure of bound peptide ligands to major histocompatibility complex

Tong, J. C., Tan, T. W. & Ranganathan, S., Sep 2004, In : Protein Science. 13, 9, p. 2523-2532 10 p.

Research output: Contribution to journalArticle

67 Citations (Scopus)

Molecular dynamics pinpoint the global fluorine effect in balanoid binding to PKCϵ and PKA

Hardianto, A., Liu, F. & Ranganathan, S., Feb 2018, In : Journal of Chemical Information and Modeling. 58, 2, p. 511-519 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Molecular modeling on the Web

Ranganathan, S., Jan 2001, In : BioTechniques. 30, 1, p. 50-52 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Molecular Modeling on the web

Ranganathan, S., 2003, Biocomputing: Computer Tools for Biologists. Stuart M. Brown (ed.). Westborough, MA: Biotechniques Press, Eaton Publishing, p. 411-417 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular similarity and diversity approaches in chemoinformatics

Khanna, V. & Ranganathan, S., Feb 2011, In : Drug Development Research. 72, 1, p. 74-84 11 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)

MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules

Govindarajan, K. R., Kangueane, P., Tan, T. W. & Ranganathan, S., 1 Feb 2003, In : Bioinformatics. 19, 2, p. 309-310 2 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions

Joo, C. T., Kong, L., Tin, W. T. & Ranganathan, S., 2006, In : Applied Bioinformatics. 5, 2, p. 111-114 4 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures

Khan, J. M., Cheruku, H. R., Tong, J. C. & Ranganathan, S., Apr 2011, In : Bioinformatics. 27, 8, p. 1192-1193 2 p., btr104.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Multiple ligand binding sites on domain seven of human complement factor H

Giannakis, E., Male, D. A., Ormsby, R. J., Mold, C., Jokiranta, T. S., Ranganathan, S. & Gordon, D. L., 2001, In : International Immunopharmacology. 1, 3, p. 433-443 11 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

MVC Architecture in Bioinformatics web applications and its Java implementation

Ranganathan, S., Bollina, D. & Lee, B. T. K., 2005, iiWAS 2005: the Seventh International Conference on Information Integration and Web-based Applications & Services : September 19-21, 2005, Kuala Lumpur, Malaysia. Kotsis, G., Tanier, D., Bressan, S., Ibrahim, I. K., Mokhtar & Salimah (eds.). Austrian Computer Society, p. 759-764 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contribution

30 Citations (Scopus)

Network analysis of human protein location

Kumar, G. & Ranganathan, S., 2010, In : BMC Bioinformatics. 11 Suppl 7, S9, p. 1-15 15 p., S9.

Research output: Contribution to journalConference paper

11 Citations (Scopus)

Oesophagostomum dentatum - Potential as a model for genomic studies of strongylid nematodes, with biotechnological prospects

Gasser, R. B., Cottee, P., Nisbet, A. J., Ruttkowski, B., Ranganathan, S. & Joachim, A., May 2007, In : Biotechnology Advances. 25, 3, p. 281-293 13 p.

Research output: Contribution to journalReview article

18 Citations (Scopus)

OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI.

Lenffer, J., Nicholas, F. W., Castle, K., Rao, A., Gregory, S., Poidinger, M., Mailman, M. D. & Ranganathan, S., 1 Jan 2006, In : Nucleic acids research. 34, Database issue, p. D599–D601 3 p.

Research output: Contribution to journalArticle

Open Access
File
42 Citations (Scopus)
32 Downloads (Pure)

PDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes

Khan, J. M. & Ranganathan, S., 2010, In : Immunome Research. 6, SUPPL. 1, p. 1-16 16 p., S2.

Research output: Contribution to journalArticle

Open Access
File
30 Citations (Scopus)
5 Downloads (Pure)

PhoglyStruct: prediction of phosphoglycerylated lysine residues using structural properties of amino acids

Chandra, A., Sharma, A., Dehzangi, A., Ranganathan, S., Jokhan, A., Chou, K-C. & Tsunoda, T., 18 Dec 2018, In : Scientific Reports. 8, p. 1-11 11 p., 17923.

Research output: Contribution to journalArticle

Open Access
File
12 Citations (Scopus)
28 Downloads (Pure)

Physiochemical property space distribution among human metabolites, drugs and toxins

Khanna, V. & Ranganathan, S., 3 Dec 2009, In : BMC Bioinformatics. 10, SUPPL. 15, p. 1-18 18 p., S10.

Research output: Contribution to journalArticle

Open Access
File
35 Citations (Scopus)
6 Downloads (Pure)

Pinpointing the putative heparin/sialic acid-binding residues in the 'sushi' domain 7 of factor H: a molecular modeling study.

Ranganathan, S., Male, D. A., Ormsby, R. J., Giannakis, E. & Gordon, D. L., 2000, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 155-167 13 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

pMHC epitope

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 1718-1719 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference book

Predicted structure of the extracellular region of ligand-gated ion- channel receptors shows SH2-like and SH3-like domains forming the ligand- binding site

Gready, J. E., Ranganathan, S., Schofield, P. R., Matsuo, Y. O. & Nishikawa, K., May 1997, In : Protein Science. 6, 5, p. 983-998 16 p.

Research output: Contribution to journalArticle

32 Citations (Scopus)

Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris

Tong, J. C., Tan, T. W., Sinha, A. A. & Ranganathan, S., 18 Dec 2006, In : BMC Bioinformatics. 7, SUPPL.5, p. 1-11 11 p., S7.

Research output: Contribution to journalArticle

Open Access
File
15 Citations (Scopus)

Prediction of HLA-DQ3.2β ligands: Evidence of multiple registers in class II binding peptides

Tong, J. C., Zhang, G. L., Tan, T. W., August, J. T., Brusic, V. & Ranganathan, S., 15 May 2006, In : Bioinformatics. 22, 10, p. 1232-1238 7 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)

Prediction of interface residue based on the features of residue interaction network

Jiao, X. & Ranganathan, S., 7 Nov 2017, In : Journal of Theoretical Biology. 432, p. 49-54 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Prediction of novel mouse TLR9 agonists using a random forest approach

Khanna, V., Li, L., Fung, J., Ranganathan, S. & Petrovsky, N., 20 Dec 2019, In : BMC Molecular and Cell Biology. 20, Suppl 2, p. 1-14 14 p., 56.

Research output: Contribution to journalArticle

Open Access
File
1 Downloads (Pure)

Proceedings, Seventh International Conference on Bioinformatics (InCoB2008) Taipei, Taiwan. 20-23 October 2008

Ranganathan, S. (ed.), Hsu, W-L. (ed.), Yang, U-C. (ed.) & Tan, T. W. (ed.), 2008, London: Springer, Springer Nature.

Research output: Book/ReportEdited Book/Anthology

Protannotator: A semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome

Islam, M. T., Garg, G., Hancock, W. S., Risk, B. A., Baker, M. S. & Ranganathan, S., 3 Jan 2014, In : Journal of Proteome Research. 13, 1, p. 76-83 8 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Protein-protein interactions and prediction: A comprehensive overview

Sowmya, G. & Ranganathan, S., 2014, In : Protein and peptide letters. 21, 8, p. 779-789 11 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Protocol for protein structure modelling

Jabeen, A., Mohamedali, A. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Cannataro, M., Gaeta, B. & Asif Khan, M. (eds.). Amsterdam; Oxford; Cambridge: Elsevier, Vol. 3. p. 252-272 21 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference book

1 Citation (Scopus)

Quantification of proteins from proteomic analysis

Noor, Z., Adhikari, S., Ranganathan, S. & Mohamedali, A., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Cannataro, M., Gaeta, B. & Asif Khan, M. (eds.). Amsterdam; Oxford; Cambridge: Elsevier, Vol. 3. p. 871-890 20 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference book

Quest for missing proteins: update 2015 on chromosome-centric human proteome project

Horvatovich, P., Lundberg, E. K., Chen, Y. J., Sung, T. Y., He, F., Nice, E. C., Goode, R. J., Yu, S., Ranganathan, S., Baker, M. S., Domont, G. B., Velasquez, E., Li, D., Liu, S., Wang, Q., He, Q. Y., Menon, R., Guan, Y., Corrales, F. J., Segura, V. & 34 others, Casal, J. I., Pascual-Montano, A., Albar, J. P., Fuentes, M., Gonzalez-Gonzalez, M., Diez, P., Ibarrola, N., Degano, R. M., Mohammed, Y., Borchers, C. H., Urbani, A., Soggiu, A., Yamamoto, T., Salekdeh, G. H., Archakov, A., Ponomarenko, E., Lisitsa, A., Lichti, C. F., Mostovenko, E., Kroes, R. A., Rezeli, M., Végvári, Á., Fehniger, T. E., Bischoff, R., Vizcaíno, J. A., Deutsch, E. W., Lane, L., Nilsson, C. L., Marko-Varga, G., Omenn, G. S., Jeong, S. K., Lim, J. S., Paik, Y. K. & Hancock, W. S., 4 Sep 2015, In : Journal of Proteome Research. 14, 9, p. 3415-3431 17 p.

Research output: Contribution to journalReview article

47 Citations (Scopus)

Radial behavior of the average local ionization energies of atoms

Politzer, P., Murray, J. S., Grice, M. E., Brinck, T. & Ranganathan, S., 1991, In : The Journal of Chemical Physics. 95, 9, p. 6699-6704 6 p.

Research output: Contribution to journalArticle

73 Citations (Scopus)

Rational structure-based drug design

Khanna, V., Ranganathan, S. & Petrovsky, N., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Ranganathan, S., Gribskov, M., Nakai, K. & Schönbach, C. (eds.). Amsterdam: Elsevier, Vol. 2. p. 585-600 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Representing Transcript Diversity in the Drosophila Melanogaster Genome using Splicing Graphs

Ranganathan, S., Lee, B. T. K. & Tan, T. W., 2004, p. 30-30. 1 p.

Research output: Contribution to conferenceAbstract

Role of solvent accessibility for aggregation-prone patches in protein folding

Mishra, A., Ranganathan, S., Jayaram, B. & Sattar, A., 27 Aug 2018, In : Scientific Reports. 8, p. 1-13 13 p., 12896.

Research output: Contribution to journalArticle

Open Access
File
6 Downloads (Pure)

SCORPION2: a database for structure-function analysis of scorpion toxins

Tan, P. T. J., Veeramani, A., Srinivasan, K. N., Ranganathan, S. & Brusic, V., 1 Mar 2006, In : Toxicon. 47, 3, p. 356-363 8 p.

Research output: Contribution to journalArticle

41 Citations (Scopus)

SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins

Kong, L., Kwong Lee, B. T., Tong, J. C., Tan, T. W. & Ranganathan, S., 1 Jul 2004, In : Nucleic acids research. 32, Suppl 2, p. W356-W359 4 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Secretome: Clues into pathogen infection and clinical applications

Ranganathan, S. & Garg, G., 30 Nov 2009, In : Genome Medicine. 1, 11, p. 1-7 7 p., 113.

Research output: Contribution to journalReview article

34 Citations (Scopus)
1 Citation (Scopus)

SGS: splicing graph server

Bollina, D., Lee, B. T. K. & Ranganathan, S., 2005, Proceedings of the 2005 International Joint Conference of InCoB, AASBi and KSBi. Lee, D., Wong, L., Kim, D-W., Kim, S., Tan, T. W. & Lee, K-H. (eds.). Korea: InCoB, AASBi and KSBi, p. 47-50 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contribution

SigPep: A Database for Signal Peptides

Choo, K. H., Ranganathan, S. & Tan, T. W., 2004, p. 12-12. 1 p.

Research output: Contribution to conferenceAbstract

Simple re-instantiation of small databases using cloud computing

Tan, T. W., Xie, C., De Silva, M., Lim, K. S., Patro, C. P. K., Lim, S. J., Govindarajan, K. R., Tong, J. C., Choo, K. H., Ranganathan, S. & Khan, A. M., 2013, In : BMC Genomics. 14, Suppl 5, p. 1-4 4 p., S13.

Research output: Contribution to journalConference paper

Open Access
File
2 Citations (Scopus)
3 Downloads (Pure)

SPdb - A signal peptide database

Choo, K. H., Tan, T. W. & Ranganathan, S., 13 Oct 2005, In : BMC Bioinformatics. 6, p. 1-8 8 p., 249.

Research output: Contribution to journalArticle

67 Citations (Scopus)

Structural bioinformatics analysis of variants on GPCR function

Syed Haneef, S. A. & Ranganathan, S., Apr 2019, In : Current Opinion in Structural Biology. 55, p. 161-177 17 p.

Research output: Contribution to journalReview article

1 Citation (Scopus)

Structural diversity of biologically interesting datasets: A scaffold analysis approach

Khanna, V. & Ranganathan, S., Aug 2011, In : Journal of Cheminformatics. 3, p. 1-14 14 p., 30.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Structural immunoinformatics: understanding MHC-Peptide-TR binding

Khan, J. M., Tong, J. C. & Ranganathan, S., 2010, Bioinformatics for immunomics. Flower, D. R., Davies, M. N. & Ranganathan, S. (eds.). New York: Springer, Springer Nature, p. 77-93 17 p. (Immunomics reviews; vol. 3).

Research output: Chapter in Book/Report/Conference proceedingChapter

Structural immunoinformatics

Ranganathan, S., Tong, J. C. & Tan, T. W., 2008, Immunoinformatics. Schönbach, C., Ranganathan, S. & Brusic, V. (eds.). New York: Springer, Springer Nature, p. 51-61 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Structural immunoinformatics

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2022-2023 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference book

Structure-based clustering of major histocompatibility complex (MHC) proteins for broad-based T-cell vaccine design

Tong, J. C., Tan, T. W. & Ranganathan, S., 2014, Immunoinformatics. De, R. K. & Tomar, N. (eds.). 2nd ed. New York: Humana Press, p. 503-511 9 p. (Methods in Molecular Biology; vol. 1184).

Research output: Chapter in Book/Report/Conference proceedingChapter