Modelling

A new version of the Sequence V1.5 software is under development for structure determination of arbitrary library compounds using mass spectrometry. The software currently has a comprehensive system for construction of library compounds and a full calculation of isotope distributions. We will apply knowledge of common high and low energy CID processes to predict fragmentations, and test these predictions experimentally using peptides that we have synthesised in the laboratory.

Left - The new version of the Sequence software. The software features a Windows graphical user interface. It enumerates libraries of full chemical structures from fragments, and is capable of handling libraries containing mixtures of linear and cyclic peptides with variable ring sizes.

We are working on models for more accurate prediction of peak intensities in CID mass spectra.

We also use bioinformatics approaches for identifying sites of potentially interesting RNA secondary structure for targeting with proteins and small molecules.

Computational chemistry is being used to assist in the design of ligands targeted to oligonucleotides. Virtual combinatorial libraries of potential ligands are assembled in silico from collections of heterocyclic fragments using bond and ring fusion operations. The two dimensional structural representations are converted into energy minimized three dimensional molecular models which are then ready for docking against a folded oligonucleotide..


	Fragments


	Join




	3D model



		2D structure


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