molecular modelling



ligfrag

Edith Chan

Computational Drug Design
Edith Chan


Tel: 
020 7679 6710
Email: edith.chan@ucl.ac.uk

My reserach interest covers all spectrum of Molecular Modelling, Computational Chemistry, Cheminformatics, Bioinformatics, and Database management. Some of the current research projects are shown below

Cheminformatics and Databases

Molecular Modelling

Drug Discovery

Academic Career

  • 2009 - present Senior Fellow, WIBR
  • 1999 - 2008 Associate Director, Molecular Design, Inpharmatics/BioFocus, UK
  • 1994 - 1999 Senior Research Scientist, Sanofi, USA
  • 1991 - 1994 Senior Scentist, Italfarmaco, Italy
  • 1991 - PhD, Cornell University, USA

Publications

Aldeghi M, Malhotra S, Selwood DL, Chan AWE. Two and Three-dimensional Rings in Drugs. Chemical Biology & Drug Design 2014, 83, 450-461.

Chan AWE, Laskowski RA, Selwood DL. Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites. J Med Chem. 2010, 53, 3086-94.

Further publication information can be viewed at https://iris.ucl.ac.uk/iris/browse/profile?upi=AWECH28

Teaching

Drug Design - MSc and MRes

Established from 2010, this course is an in depth study of modern drug design methods from bioinformatics to molecular modeling and fragment based drug design. Sections on intellectual property and marketing provide a solid background for anyone considering a career in the pharmaceutical and health industries.

Here is a list of commerical and academic software, databases and programs that we use. We are grateful that these organisations and their scientists grant us the permission to use them.

Software

Comprehensive:

*MOE (CCG) - Comprehensive computational software for Drug Discovery process

Molecular Modeling/Cheminformatics:

* Pipeline Pilot (Accelrys)- Comprehensive cheminformatics tools 

* Cresset Field Technolgy - molecular Field technology 

* GOLD (CCDC) - Protein-Ligand Docking 

* YASARA (Yasara) - Modeling and SImulation 

Accelrys Draw (Accelrys) - Chemical structure drawing tool, Tutorial

COOT - Crystallographic Object-Oriented Toolkit

Bioinformatics:

BioEdit - Biological sequence alignment editor 

PyMOL - Open-source molecular graphics visualisation, PyMOL examples

RasMol - Molecular graphics visualisation 

Swiss-Pdb Viewer - PDB viewer

Others:

Origin (OriginLab) - Data analysis, publication-quality graphing, and programming. 

Databases

Codon usage database - Codon usage database 

DrugBank - Drug/Target information 

EBI - EBI home 

ExPASy - ExPASy proteomics server 

NCBI - NCBI home 

PDB - Research Collaboratory for Structural Bioinformatics (RCSB) 

PDBsum - Summaries and structural analyses of PDB data files 

Swiss-Prot - Protein sequence and function 

Mobyle@pasteur - codon calculation 

UniProt - Protein sequence and function 

Web programs

NCBI Blast - Similarity between biological sequences 

Optimizer - Optimize a DNA or protein sequence 

phyre - Protein Homology/analogY Recognition Engine 

RaCC - Rare Codon Calculator 

Rare codon search (Bioline)

Studentship/job links

New scientist study 

Find a PhD 

Postgraduate studentships

Nature jobs/studentships

Science jobs/studentships 

New scientist jobs 

UK academic jobs (jobs.ac.uk)

* Commercial and require license. Otherwise, most software listed here is free to download for academic use.