Digital Imaging Research Centre | Mobile Information & Network Technologies Centre | Jean-Christophe Nebel

Nestor3D Free Protein 3D Pattern Generation Software Version: 1.0 beta, 2004-2008 Author: J-C Nebel

About Nestor3D

What?

Nestor3D is a free software allowing the multiple alignment of a set of protein structures containing either ligands, prosthetic groups or PROSITE patterns.
It can generate:

• description of the cavity associated with either a ligand or a prosthetic group.

• consensus 3D pattern including atom, chemical group and cavity positions

• similarity matrix

Why?

Nestor3D can be used for many different applications:

• better understanding of active sites
  • 3D patterns including atom, chemical group and cavity positions provide new insight into active sites

• protein functional annotation
  • detection of putative active sites from a protein 3D structure
  • generation of phylogenetic tree from similarity matrix

• homology modelling
  • generation of a template of a protein structure from a consensus structure produced from a set of 3D structures of homologue proteins
  • validation of predicted protein structure by checking the similarity of its active sites with known structures

• drug design
  • generation of a template of the structure of the active site of a protein

• sequence alignment
  • knowledge than structural elements are aligned at the structural level can be used to refine sequential alignments

How?

At the heart of Nestor3D, there is a new method which is based on the comparison of sets of homologue proteins the 3D structures of which are known. Protein structures are aligned according to the position of rigid elements of either ligands, prosthetic groups or PROSITE patterns. Then, from that multiple alignment, a consensus 3D pattern is produced. It contains three different types of structural information: atom, chemical group and cavity 3D positions.

Where?

Nestor3D can be dowloaded for free from the following address: www.staffnet.ac.uk/~ku33185/Nestor3D.html

Who?

The author is Jean-Christophe Nebel from Kingston University, London. If you use Nestor3D in a publication please cite one of the following papers:

Generation of 3D templates of active sites of proteins with rigid prosthetic groups, J.-C. Nebel, Bioinformatics Advance Access published online on 10 February 2006, Bioinformatics [PDF]
Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position, J.-C. Nebel, BMC Bioinformatics 2005, 6(Suppl 3):S10, Bioinformatics & Systems Biology Conference, Oral presentation, 14-15 July 2005, Edinburgh, Scotland, UK [PDF]

Example

3D template of the active site of CYP17

The model is based on the 3D structures of 5 homologue proteins (1PQ2, 1W0G, 1BU7, 1H5Z and 1N97) aligned according to the position of the haem group which is involved in their active site.

(Group colour scheme) Acidic Basic Sulfur (cysteine) OH group CO group Aromatic ring Non Polar

 

Download

Download Nestor3D Now! version 1.0 beta (July 2005)
Free download 2.10MB

Manual (v1.0b)

Please click here in order to register your interest.
By registering you support further development and will be informed about future updates of Nestor3D.

The Nestor3D software requires you are able to execute Java programs on your system. If you don't have Java 1.5 or later, it can be downloaded for free from the java.sun.com web site.

Troubleshooting

The main common cause of problems comes from non-standard PDB entries. Please, check the files you wish to use and edit them if required.

Please email me if you would like to report a bug, if you have troubles using Nestor3D or if you have any suggestion: j.nebel@kingston.ac.uk.

Keywords

Structural Bioinformatics, Protein, 3D Structure, Binding Site, Active Site, Consensus, 3D Pattern, 3D Motif, Protein Structure Prediction, Protein Function Prediction, Drug Design, Docking  

Publications

Copyright notice: This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit permission of the copyright holder.

• Detection and annotation of ligand binding sites based on atomic descriptors, J.-C. Nebel, Protein Sequence, structure and function (Biochemical Society / Wellcome Trust Focused Meeting), January 2009, Hinxton, UK, poster [PDF]

• Automatic generation of 3D motifs for classification of protein binding sites, J.-C. Nebel, P. Herzyk and D. R. Gilbert, BMC Bioinformatics, 8:32, 2007 [PDF]

• Generation of 3D templates of active sites of proteins with rigid prosthetic groups, J.-C. Nebel, Bioinformatics, 22(10):1183-1189, 2006 [PDF]

• Generation of 3D templates of active sites of proteins with rigid prosthetic groups, J.-C. Nebel, GCB'05: German Conference on Bioinformatics, 5-7 October 2005, Hamburg, Germany [PDF]
• Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position, J.-C. Nebel, BMC Bioinformatics 2005, 6(Suppl 3):S10, Bioinformatics & Systems Biology Conference, Oral presentation, 14-15 July 2005, Edinburgh, Scotland, UK [PDF]
• Modelling of P450 active site based on consensus 3D structures, J.-C. Nebel, International Conference on Biomedical Engineering, BioMed 2005, 16-18 February 2005, Innsbruck, Austria [PDF]