MSc - Molecular Modelling and Bioinformatics

A full-time course over one year

A part-time course over two years

Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX
For further information contact: C Burton, Telephone 0171 631 6800, e.mail c.burton@mail.cryst.bbk.ac.uk

Chairman of Examiners: Dr Beatrice Gorinsky
Course Organiser: Dr Beatrice Gorinsky

Course Tutors:
Prof. J M Goodfellow
Dr D S Moss
Dr. I Tickle
Dr. H R Saibil

INTRODUCTION

The MSc course is designed for students who are particularly interested in the use of computational techniques in the study of molecular and biological science. This course can be taken full-time over one year or part-time over two years of study, and provides a unique training for graduates with degrees in physical, chemical or biological sciences. The emphasis is on the practical application of these techniques to a variety of problems in the field of molecular modelling, both static and dynamic. Teaching is principally by members of the Crystallography Department, although lecturers from other universities and from industry are invited to supplement our courses in specific areas and describe techniques for which they are internationally recognised. The course provides training that is relevant to industries that are concerned with the use and development of computer software, such as the chemical, computer and pharmaceutical industries.

AIMS OF THE COURSE

To train students in the use of computational techniques in the study of molecular and biological science.

OBJECTIVES OF THE COURSE



CURRICULUM

The course is divided into modules covering eight main fields of study, together with associated tutorials. For part-time students the course runs in 3 hour sessions on two evenings per week from 6.00pm-9.00pm. Presently these sessions are scheduled for Monday and Thursday evenings. Students may be asked to attend on a third evening in the first term. Full- time students also attend lectures and practical sessions during the day. The modules in this course are:
Most course units involve coding programs in C/C++, and using software packages on workstations. Practical exercises and written and oral dissertations are an integral part of most modules. There is emphasis on transferable skills such as group course work, in which the students learn collaborative skills, and self-paced learning with increasing use of Internet and the World Wide Web. Students gain practical experience of molecular modelling software and the use of databases. Tutorials are given in the first term on specific mathematical topics relevant to the course, and in the penultimate term there are a series of general tutorials. Revision lectures on all course units are given in the final term. Students accepted on the course with little or no biological background must follow an additional reading program.

PROJECTS

Full-time and part-time students undertake projects in areas of expertise within the department supervised by members of staff, or occasionally by external supervisors. Project areas include: Students may undertake a project of personal interest providing that it is approved and a member of staff is prepared to act as the internal supervisor.

DETAILS OF COURSE MODULES

  1. Introduction to Biocomputing

    This module is designed to introduce students to modern concepts of software construction and to algorithms used in biocomputing. Students are introduced to the elementary principles of software design and to object oriented programming concepts. They learn to use a subset of C++ and simple class libraries of objects such as atoms, molecules, sequences and graphical user interfaces. Algorithms are introduced for the alignment and comparison of macromolecular structures. Both PCs and workstations are used in this module and students become familiar with both Windows and Unix operating systems and are introduced to Java.

  2. Databases in Molecular Science

    Students are introduced through a guided exploration of WWW resources to the practical use and design of databases. Data formats and information are reviewed and fundamental algorithms for data storage and retrieval are discussed together with the use of Internet tools.

  3. Molecular Interactions including Introduction to Quantum Mechanics

    This module covers the development and application of potential energy functions to biological molecules. Part of the unit is a short project for which individual students develop a program to implement a potential energy function for a simple molecule and apply energy minimization.
    The treatment of electrostatic interactions are emphasized and the use of quantum mechanics to study molecular interactions is introduced. Basic concepts are reviewed and some applications are descibed.

  4. Fourier Analysis, Diffraction Theory and Image Processing

    Fourier transform theory underlies many techniques for determining molecular structure including X-ray and neutron crystallography, fibre diffraction, NMR spectroscopy and image processing. The basic theory and its application to image processing in electron microscopy, computer tomography and protein structure determination will be discussed. Practical use will be made of FFT algorithms and image processing software.

  5. Molecular Structure and Graphics

    With the large number of protein structures currently available it is now possible to categorize these structures and their building blocks from which binding sites and function may sometimes be deduced. The principles of protein structure and packing are reviewed and the structures of nucleic acids are discussed. Structures of current interest are reviewed by the students in a series of oral presentations. Students gain practical experience of Unix machines and a range of graphics software packages including 'O', Quanta, Sybyl, Prepi, Grasp, VMD, RasMol, and Molscript.

  6. Computer Architecture and Operating Systems

    This module aims to review conventional computer hardware and software, as well as contrasting these with high speed computers using vector and parallel architectures such as the CRAY, and INTEL Hypercube. Software developments such as Fortran90 and message passing code are also described with reference to applications relevant to other units.

  7. Dynamic Processes of Molecular and Biological Systems

    Time dependent processes are an essential part of the behaviour of molecules. We focus on two aspects namely the molecular dynamics of macromolecules and enzyme kinetics. Both processes can be approached theoretically but are so complicated that approximate numerical solutions are required. This unit covers the many applications to the conformation, flexibility and thermodynamics of molecules as well as the use of the major software packages.

  8. Introduction to Protein Sequence Analysis

    This course is designed to introduce students to some basic theoretical and practical aspects of protein sequence analysis. The different types of biological database are reviewed, and the major bioinformatics resource centres are mentioned. The principal sequence anaylsis methods that underpin pattern databases are outlined, introducing concepts such as scoring matrices, the Twilight Zone, signal to noise, and biological vs mathematical significance. Students are taught how to build their own sequence analysis strategies, without recourse to commercial packages. This approach is supported by means of a WWW-based practical: this is a self paced tutorial in which an unknown fragment of DNA is used to search sequence, pattern, and structure databases, in order to identify the protein coded for and to learn about its structure and function.


EXAMINATION

This MSc course will be examined by:


The written examinations will take place in May or June and the oral examination in September. Coursework from all sections of the syllabus will be assessed throughout the course and will include practical computing. The current examiners are: Prof D Jackson (Pharmacy Department, Nottingham) Prof J M Goodfellow (Crystallography Department, Birkbeck) Dr B Gorinsky (Crystallography Department, Birkbeck) Dr D S Moss (Crystallography Department, Birkbeck) Prof P Murray-Rust (Glaxo, Visiting Professor at Birkbeck)

COMPUTER AND GRAPHICS FACILITIES

We have access to a full range of computer facilities ranging from PC's to supercomputers. The College has a VAX 6310 and 30 IBM Model PS/2 PC's which are networked to JANET/JIPS. There are also a number of RS6000 workstations. The Department is continually expanding and upgrading its computing facilities, which are available to our MSc students. These include a network of UNIX workstations including high performance HP735, Silicon Graphics Indigos and Dec; PC-486 and Pentiums are used for software development, access to databases and word processing. They also provide access to Internet.

There is a dedicated MSc computer laboratory which has been upgraded as part of the refurbishment of the Crystallography Department and a new visualisation laboratory and multimedia seminar room, equipped with graphics workstations, funded through a grant made by Glaxo.


ENTRY QUALIFICATIONS

A degree in the physical, chemical or biological sciences is desirable, but consideration will be given to candidates with degrees in mathematics, computing, engineering or other allied subjects. On entry students are required to have some practical knowledge of one programming language. Students should ideally have A-level mathematics or the equivalent, but candidates with O-level or GCSE mathematics will be considered.

FULL-TIME STUDENTS

Full-time students are encouraged to attend relevant Departmental lectures given by visiting experts from industry and academia, also the appropriate sections of the Graduate Studies program run by the Department.

SPONSORSHIP

This MSc is recognised as an advanced course by the Biotechnology and Biological Sciences Research Council, who has given a limited number of grants for full-time students. Applicants wishing to apply for a studentship should have a first or upper 2 degree.

CRYSTALLOGRAPHY DEPARTMENT

This is a multidisciplinary department comprising biologists, biochemists, chemists, crystallographers, physists and mathematicians all with an interest in molecular structure, both static and dynamic. Computational techniques link the wide range of Departmental research interests and this MSc course has evolved directly from our basic use of computers in the study of molecular structure in all its aspects. Historically the department originated with the Biomolecular Research Laboratory directed by Professor J D Bernal in 1948. This laboratory included a centre for the construction and use of one of the first valve computers built by Dr A D Booth.

BIRKBECK COLLEGE

Birkbeck College was founded in 1823 and incorporated by Royal Charter in 1926 as one of the multi-faculty schools of the University of London and specialises in evening courses designed for part-time students. Currently over half of the students in the College are postgraduates. Lectures take place on weekday evenings between 6.00pm and 9.00pm. College facilities, including the library, cafeteria, snack-bar, bar and nursery are open every weekday evening.

ACKNOWLEDGEMENTS

This booklet was produced by Beatrice Gorinsky with the help of other members of the department which is gratefully acknowledged.

NOTE

This booklet should be read in conjunction with the College Prospectus and the information it contains is subject to the terms and conditions set out in the College Prospectus. The information contained in this booklet is correct at time of publication.