Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W128-32.

3dSS: 3D structural superposition.

Sumathi K, Ananthalakshmi P, Roshan MN, Sekar K.

Source

Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.

Abstract

3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed 3D atomic coordinates in the client machine. To perform the above, users need to enter Protein Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB format. This server uses a locally maintained PDB anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/3dss/ or http://10.188.1.15/3dss/.

PMID:: 16844975; [PubMed - indexed for MEDLINE]
PMCID:: PMC1538824

Free PMC Article

Images from this publication.See all images (4) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

3DSS - Bioinformatics.ca Links Directory

Supplemental Content

Save items

Related citations in PubMed

BSDD: Biomolecules Segment Display Device--a web-based interactive display tool. [Nucleic Acids Res. 2004]
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool.
Selvarani P, Shanthi V, Rajesh CK, Saravanan S, Sekar K. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W645-8.
SuperPose: a simple server for sophisticated structural superposition. [Nucleic Acids Res. 2004]
SuperPose: a simple server for sophisticated structural superposition.
Maiti R, Van Domselaar GH, Zhang H, Wishart DS. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W590-4.
SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules. [Nucleic Acids Res. 2003]
SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules.
Hussain AS, Kumar ChK, Rajesh CK, Sheik SS, Sekar K. Nucleic Acids Res. 2003 Jul 1; 31(13):3356-8.
PSST-2.0: Protein Data Bank Sequence Search Tool. [Appl Bioinformatics. 2005]
PSST-2.0: Protein Data Bank Sequence Search Tool.
Ananthalakshmi P, Samayamohan K, Chokalingam C, Mayilarasi C, Sekar K. Appl Bioinformatics. 2005; 4(2):141-5.
LySDB - Lysozyme Structural DataBase. [Acta Crystallogr D Biol Crysta...]
LySDB - Lysozyme Structural DataBase.
Mohan KS, Das S, Chockalingam C, Shanthi V, Sekar K. Acta Crystallogr D Biol Crystallogr. 2004 Mar; 60(Pt 3):597-600. Epub 2004 Feb 25.

See reviews... See all...

Cited by 3 PubMed Central articles

Evaluation of an antimicrobial L-amino acid oxidase and peptide derivatives from Bothropoides mattogrosensis pitviper venom. [PLoS One. 2012]
Evaluation of an antimicrobial L-amino acid oxidase and peptide derivatives from Bothropoides mattogrosensis pitviper venom.
Okubo BM, Silva ON, Migliolo L, Gomes DG, Porto WF, Batista CL, Ramos CS, Holanda HH, Dias SC, Franco OL, et al. PLoS One. 2012; 7(3):e33639. Epub 2012 Mar 16.
Structure of the MthK RCK in complex with cadmium. [J Struct Biol. 2010]
Structure of the MthK RCK in complex with cadmium.
Dvir H, Valera E, Choe S. J Struct Biol. 2010 Aug; 171(2):231-7. Epub 2010 Apr 4.
Using least median of squares for structural superposition of flexible proteins. [BMC Bioinformatics. 2009]
Using least median of squares for structural superposition of flexible proteins.
Liu YS, Fang Y, Ramani K. BMC Bioinformatics. 2009 Jan 22; 10:29. Epub 2009 Jan 22.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

3dSS: 3D structural superposition.
3dSS: 3D structural superposition.
Nucleic Acids Res. 2006 Jul 1 ;34(Web Server issue):W128-32.

PubMed
Transient global amnesia after gastroscopy.
Transient global amnesia after gastroscopy.
J Neurol Neurosurg Psychiatry. 2006 Aug ;77(8):995-6.

PubMed
Antioxidant vitamin therapy alters sepsis-related apoptotic myocardial activity ...
Antioxidant vitamin therapy alters sepsis-related apoptotic myocardial activity and inflammatory responses.
Am J Physiol Heart Circ Physiol. 2006 Dec ;291(6):H2779-89. Epub 2006 Jul 14 .

PubMed
Commentary: the higher standards of aspirational ethics.
Commentary: the higher standards of aspirational ethics.
J Am Acad Psychiatry Law. 2006 ;34(2):242-4.

PubMed
Glycolipid alpha-C-galactosylceramide is a distinct inducer of dendritic cell fu...
Glycolipid alpha-C-galactosylceramide is a distinct inducer of dendritic cell function during innate and adaptive immune responses of mice.
Proc Natl Acad Sci U S A. 2006 Jul 25 ;103(30):11252-7. Epub 2006 Jul 14 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: