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Items: 1 to 20 of 159


PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

Gandhimathi A, Ghosh P, Hariharaputran S, Mathew OK, Sowdhamini R.

Nucleic Acids Res. 2015 Nov 8. pii: gkv1205. [Epub ahead of print]


Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R.

Brief Bioinform. 2015 Oct 22. pii: bbv084. [Epub ahead of print]


Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.

Kaushik S, Nair AG, Mutt E, Subramanian HP, Sowdhamini R.

Bioinformatics. 2015 Oct 10. pii: btv538. [Epub ahead of print]


PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots.

Sukhwal A, Sowdhamini R.

Bioinform Biol Insights. 2015 Sep 21;9:141-51. doi: 10.4137/BBI.S25928. eCollection 2015.


A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities.

Ghosh P, Grellscheid SN, Sowdhamini R.

J Biomol Struct Dyn. 2015 Nov 26:1-8. [Epub ahead of print]


Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.

Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R.

BMC Plant Biol. 2015 Aug 28;15:212. doi: 10.1186/s12870-015-0562-x.


Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.

Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.


An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway.

Mahita J, Harini K, Rao Pichika M, Sowdhamini R.

J Biomol Struct Dyn. 2015 Sep 2:1-18. [Epub ahead of print]


Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening.

Harini K, Sowdhamini R.

PLoS One. 2015 Jul 29;10(7):e0131077. doi: 10.1371/journal.pone.0131077. eCollection 2015.


SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.

Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL, Srinivasan N.

Database (Oxford). 2015 Jun 30;2015:bav060. doi: 10.1093/database/bav060. Print 2015.


172 Computational analysis and prediction of proteins that undergo domain swapping.

Shingate P, Upadhyay A, Khader S, Sowdhamini R.

J Biomol Struct Dyn. 2015 May;33 Suppl 1:112-3. doi: 10.1080/07391102.2015.1032809. No abstract available.


161 Bridging the islands of protein families in sequence space using artificial sequences.

Srinivasan N, Mudgal R, Kumar G, Chandra NR, Sowdhamini R, Sandhya S.

J Biomol Struct Dyn. 2015 May;33 Suppl 1:103-4. doi: 10.1080/07391102.2015.1032798. No abstract available.


Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.

Shingate P, Warwicker J, Sowdhamini R.

PLoS One. 2015 Jun 4;10(6):e0127716. doi: 10.1371/journal.pone.0127716. eCollection 2015.


Mechanistic Basis Of Peptide-Protein Interaction In AtPep1-PEPR1 Complex In Arabidopsis thaliana.

Raghavender US, Sowdhamini R.

Protein Pept Lett. 2015;22(7):618-27.


DOCKSCORE: a webserver for ranking protein-protein docked poses.

Malhotra S, Mathew OK, Sowdhamini R.

BMC Bioinformatics. 2015 Apr 24;16:127. doi: 10.1186/s12859-015-0572-6.


Key challenges for the creation and maintenance of specialist protein resources.

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.

Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.


Collation and analyses of DNA-binding protein domain families from sequence and structural databanks.

Malhotra S, Sowdhamini R.

Mol Biosyst. 2015 Apr;11(4):1110-8. doi: 10.1039/c4mb00629a.


POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.

Shameer K, Naika MB, Mathew OK, Sowdhamini R.

Bioinform Biol Insights. 2014 Dec 21;8:209-14. doi: 10.4137/BBI.S19057. eCollection 2014.


Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies.

Gupte TM, Haque F, Gangadharan B, Sunitha MS, Mukherjee S, Anandhan S, Rani DS, Mukundan N, Jambekar A, Thangaraj K, Sowdhamini R, Sommese RF, Nag S, Spudich JA, Mercer JA.

J Biol Chem. 2015 Mar 13;290(11):7003-15. doi: 10.1074/jbc.M114.596676. Epub 2014 Dec 29.

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