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Results: 1 to 20 of 133

1.

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(1):303. [Epub ahead of print]

PMID:
25228146
[PubMed - as supplied by publisher]
Free Article
2.

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
3.

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
4.

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
5.

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]
6.

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 - in process]
Free PMC Article
7.

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]
8.

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 Article
9.

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
10.

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]
11.

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]
12.

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
13.

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
14.

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]
15.

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]
16.

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
17.

STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice.

Naika M, Shameer K, Mathew OK, Gowda R, Sowdhamini R.

Plant Cell Physiol. 2013 Feb;54(2):e8. doi: 10.1093/pcp/pcs185. Epub 2013 Jan 10.

PMID:
23314754
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus.

Manoharan M, Ng Fuk Chong M, Va├»tinadapoul├ę A, Frumence E, Sowdhamini R, Offmann B.

Genome Biol Evol. 2013;5(1):163-80. doi: 10.1093/gbe/evs131.

PMID:
23292137
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships.

Syamaladevi DP, Sunitha MS, Kalaimathy S, Reddy CC, Iftekhar M, Pasha SN, Sowdhamini R.

Bioinform Biol Insights. 2012;6:247-54. doi: 10.4137/BBI.S9902. Epub 2012 Nov 12.

PMID:
23189029
[PubMed]
Free PMC Article
20.

Integrative structural modelling of the cardiac thin filament: energetics at the interface and conservation patterns reveal a spotlight on period 2 of tropomyosin.

Margaret Sunitha S, Mercer JA, Spudich JA, Sowdhamini R.

Bioinform Biol Insights. 2012;6:203-23. doi: 10.4137/BBI.S9798. Epub 2012 Oct 3.

PMID:
23071391
[PubMed]
Free PMC Article

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