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Results: 1 to 20 of 138

1.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function.

Ramakrishnan G, Ochoa-MontaƱo B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N.

Tuberculosis (Edinb). 2014 Nov 6. pii: S1472-9792(14)20511-7. doi: 10.1016/j.tube.2014.10.009. [Epub ahead of print] Review.

PMID:
25467293
[PubMed - as supplied by publisher]
2.

Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages.

Kaushik S, Sowdhamini R.

BMC Genomics. 2014 Nov 18;15(1):985. [Epub ahead of print]

PMID:
25407321
[PubMed - as supplied by publisher]
Free Article
3.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.

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

Nucleic Acids Res. 2014 Sep 27. pii: gku888. [Epub ahead of print]

PMID:
25262355
[PubMed - as supplied by publisher]
Free Article
4.

Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes.

Malhotra S, Sowdhamini R.

Bioinform Biol Insights. 2014 Sep 10;8:193-8. doi: 10.4137/BBI.S16313. eCollection 2014.

PMID:
25249757
[PubMed]
Free PMC Article
5.

ECMIS: computational approach for the identification of hotspots at protein-protein interfaces.

Shingate P, Manoharan M, Sukhwal A, Sowdhamini R.

BMC Bioinformatics. 2014 Sep 16;15:303. doi: 10.1186/1471-2105-15-303.

PMID:
25228146
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

DOR - a Database of Olfactory Receptors - Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes.

Nagarathnam B, Karpe SD, Harini K, Sankar K, Iftekhar M, Rajesh D, Giji S, Archunan G, Balakrishnan V, Gromiha MM, Nemoto W, Fukui K, Sowdhamini R.

Bioinform Biol Insights. 2014 Jun 12;8:147-58. doi: 10.4137/BBI.S14858. eCollection 2014.

PMID:
25002814
[PubMed]
Free PMC Article
7.

Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways.

Gupta GD, Dey G, Swetha MG, Ramalingam B, Shameer K, Thottacherry JJ, Kalappurakkal JM, Howes MT, Chandran R, Das A, Menon S, Parton RG, Sowdhamini R, Thattai M, Mayor S.

PLoS One. 2014 Jun 27;9(6):e100554. doi: 10.1371/journal.pone.0100554. eCollection 2014.

PMID:
24971745
[PubMed - in process]
Free PMC Article
8.

3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.

Joseph AP, Shingate P, Upadhyay AK, Sowdhamini R.

Database (Oxford). 2014 Apr 3;2014:bau026. doi: 10.1093/database/bau026. Print 2014.

PMID:
24700812
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations.

Kaushik S, Etchebest C, Sowdhamini R.

Proteins. 2014 Jul;82(7):1428-43. doi: 10.1002/prot.24511. Epub 2014 Feb 6.

PMID:
24500901
[PubMed - in process]
10.

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

Malhotra S, Sankar K, Sowdhamini R.

PLoS One. 2014 Feb 3;9(2):e80255. doi: 10.1371/journal.pone.0080255. eCollection 2014.

PMID:
24498255
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability.

Mudgal R, Sowdhamini R, Chandra N, Srinivasan N, Sandhya S.

J Mol Biol. 2014 Feb 20;426(4):962-79. doi: 10.1016/j.jmb.2013.11.026. Epub 2013 Dec 4.

PMID:
24316367
[PubMed - indexed for MEDLINE]
12.

Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies.

Mutt E, Rani SS, Sowdhamini R.

BioData Min. 2013 Nov 15;6(1):20. doi: 10.1186/1756-0381-6-20.

PMID:
24237883
[PubMed]
Free PMC Article
13.

LenVarDB: database of length-variant protein domains.

Mutt E, Mathew OK, Sowdhamini R.

Nucleic Acids Res. 2014 Jan;42(Database issue):D246-50. doi: 10.1093/nar/gkt1014. Epub 2013 Nov 4.

PMID:
24194591
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Investigations of Ramachandran disallowed conformations in protein domain families.

Lakshmi B, Ramakrishnan C, Archunan G, Sowdhamini R, Srinivasan N.

Int J Biol Macromol. 2014 Feb;63:119-25. doi: 10.1016/j.ijbiomac.2013.10.032. Epub 2013 Oct 31.

PMID:
24184732
[PubMed - indexed for MEDLINE]
15.

Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations.

Manoharan M, Fuchs PF, Sowdhamini R, Offmann B.

J Biomol Struct Dyn. 2014;32(11):1742-51. doi: 10.1080/07391102.2013.834118. Epub 2013 Sep 13.

PMID:
24028686
[PubMed - in process]
16.

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins.

Syamaladevi DP, Joshi A, Sowdhamini R.

Bioinformation. 2013 Jun 8;9(10):491-9. doi: 10.6026/97320630009491. Print 2013.

PMID:
23861564
[PubMed]
Free PMC Article
17.

Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions.

Malhotra S, Sowdhamini R.

Nucleic Acids Res. 2013 Aug;41(15):7212-9. doi: 10.1093/nar/gkt505. Epub 2013 Jun 17.

PMID:
23775796
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

Naika M, Shameer K, Sowdhamini R.

Mol Biosyst. 2013 Jul;9(7):1888-908. doi: 10.1039/c3mb70072k. Epub 2013 May 3.

PMID:
23645342
[PubMed - indexed for MEDLINE]
19.

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies.

Sukhwal A, Sowdhamini R.

Mol Biosyst. 2013 Jul;9(7):1652-61. doi: 10.1039/c3mb25484d. Epub 2013 Mar 27.

PMID:
23532342
[PubMed - indexed for MEDLINE]
20.

Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage.

Kaushik S, Mutt E, Chellappan A, Sankaran S, Srinivasan N, Sowdhamini R.

PLoS One. 2013;8(2):e56449. doi: 10.1371/journal.pone.0056449. Epub 2013 Feb 20.

PMID:
23437136
[PubMed - indexed for MEDLINE]
Free PMC Article

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