Limits...
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM - Acta Crystallogr. D Biol. Crystallogr. (2013)

Bottom Line: Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources.LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed.Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England.

ABSTRACT
Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Show MeSH
A plot of the top-scoring molecules in each of the 47 clusters returned by LigSearch for UniProt entry P65248. The molecules have been laid out using multi-dimensional scaling on the basis of their all-by-all similarities. Thus, similar molecules tend to be grouped together. The labels show the cluster number in square brackets and the PDB Het Group three-character name or ChEBI identifier. Red labels correspond to molecules from matches to PDB entries, while blue labels are molecules returned by ChEBI searches. The molecular diagrams were plotted using ChemDraw (http://www.cambridgesoft.com).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3852652&req=5

fig3: A plot of the top-scoring molecules in each of the 47 clusters returned by LigSearch for UniProt entry P65248. The molecules have been laid out using multi-dimensional scaling on the basis of their all-by-all similarities. Thus, similar molecules tend to be grouped together. The labels show the cluster number in square brackets and the PDB Het Group three-character name or ChEBI identifier. Red labels correspond to molecules from matches to PDB entries, while blue labels are molecules returned by ChEBI searches. The molecular diagrams were plotted using ChemDraw (http://www.cambridgesoft.com).

Mentions: The clustering of all of the candidate molecules by SMSD resulted in 47 separate clusters, five of which contained a single metal ion. Fig. 3 ▶ shows the highest-scoring members of each of these 47 clusters plotted using multi-dimensional scaling on the basis of their all-by-all similarities.


LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM - Acta Crystallogr. D Biol. Crystallogr. (2013)

A plot of the top-scoring molecules in each of the 47 clusters returned by LigSearch for UniProt entry P65248. The molecules have been laid out using multi-dimensional scaling on the basis of their all-by-all similarities. Thus, similar molecules tend to be grouped together. The labels show the cluster number in square brackets and the PDB Het Group three-character name or ChEBI identifier. Red labels correspond to molecules from matches to PDB entries, while blue labels are molecules returned by ChEBI searches. The molecular diagrams were plotted using ChemDraw (http://www.cambridgesoft.com).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852652&req=5

fig3: A plot of the top-scoring molecules in each of the 47 clusters returned by LigSearch for UniProt entry P65248. The molecules have been laid out using multi-dimensional scaling on the basis of their all-by-all similarities. Thus, similar molecules tend to be grouped together. The labels show the cluster number in square brackets and the PDB Het Group three-character name or ChEBI identifier. Red labels correspond to molecules from matches to PDB entries, while blue labels are molecules returned by ChEBI searches. The molecular diagrams were plotted using ChemDraw (http://www.cambridgesoft.com).
Mentions: The clustering of all of the candidate molecules by SMSD resulted in 47 separate clusters, five of which contained a single metal ion. Fig. 3 ▶ shows the highest-scoring members of each of these 47 clusters plotted using multi-dimensional scaling on the basis of their all-by-all similarities.

Bottom Line: Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources.LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed.Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England.

ABSTRACT
Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Show MeSH