Division of Molecular Biosciences
Department of Life Sciences
Faculty of Natural Sciences

Dr Suhail A Islam

Role

Dr Islam is the Computer Systems Manager for a number of research groups at Imperial College London. These include groups of Professors Michael J.E. Sternberg, Michael Stumpf, Xiaodong Zhang, Paul Freemont and Dr Robert Endres. Main responsibilities include:

  • Evaluation and procurement of hardware and software
  • Installation and maintenance of hardware (destops, servers, clusters, laptops)
  • Installation and maintenance of software (OSs, Developments tools, MySQL databases, WEB servers)
  • Management of Linux computer farms (approximately 400 cores)
  • Daily management of systems (linux, macs & pcs) and user administration

Teaching and Training

Teaching duties include-
Undergraduate - practicals in molecular graphics and data analysis using Excel
Post-graduate training - IT induction (2 day course concentrating mainly on Linux)
Post-graduate teaching - Molecular Graphics.

Research Interests

I maintain a strong interest in Computer Graphics and computational structural biology (please see list of publications). Previous major projects include:

  • PREPI (Protein Representations Interactively). This is a Molecular Graphics package for the display of proteins and nucleic acids. Program was originally developed for the Silicon Graphics platform using GL

  • IMAGE3D Suite- software for image reconstruction from confocal microscopy. A computational suite of programs developed for the quantitative analysis of cell nucleus organisation.

    C. Shiels, S.A. Islam, R. Vatcheva, P. Sasieni, M. J. E. Sternberg, D. Sheer and P.S. Freemont
    PML bodies associate specifically with the MHC gene cluster in interphase nuclei
    J.Cell Sci. 114: 3705-3716 (2001)
    Wang J, Shiels C, Sasieni P, Wu PJ, Islam SA, Freemont PS, Sheer D
    Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions
    J Cell Biol 164(4) 16 Feb 2004
    McManus KJ, Stephens DA, Adams NM, Islam SA, Freemont PS, Hendzel MJ
    The transcriptional regulator CBP has defined spatial associations phase nuclei
    PLoS Comput Biol 2(10) 20 Oct 2006
    Shiels C, Adams NM, Islam SA, Stephens DA, Freemont PS
    Quantitative analysis of cell nucleus organisation
    PLoS Comput Biol 3(7) Jul 2007

  • Protein Domain Server The concept of a domain is central to taxonomy, comparision and prediction of protein three-dimensional structure. An algorithm (called DAD) has been developed to identify the location of domains in proteins. This web server provides a database of protein domain assignments ( as defined by Authors and also by DAD). Users may also compute domain assignments for their own coordinate data.

    Suhail A Islam, Jingchu Luo and Michael J E Sternberg
    Identification and analysis of domains in proteins Protein Engineering Vol. 8 no.6 pp 513-525, 1995
    Michael JE Sternberg, Hedvig Hegyi, Suhail A Islam, Jingchu Luo and Robert B Russell
    Towards an Intellegent System for the Automatic Assignment of Domains in Globular Proteins. In "ISMB-95 Proceedings Third International Conference on Intelligent Systems For Molecular Biology" Eds. C. Rawlings et al. pp 376-383, 1995. AAAI Press, Menlo Park, California

  • Heavy-Atom Databank This databank contains details of experimental conditions used for protein crystallization, including details on compounds, pH ranges etc. There is also structural information on the binding sites (protein environment in crystal and solvent) of heavy atoms (e.g. HG, PT, U). This databank will be of interest not only to protein crystallographers but to anyone interested in the interaction of heavy-atoms with proteins.

    Carivn, D, Islam, S.A., Sternberg, M.J.E. and Blundell, T.L
    HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: A Resourse for Use in Multiple Isomorphous Replacement and Anomalous Scattering. Acta. Cryst. (1998). D54, 1199-1206
    Carvin, D, Islam, S.A., Sternberg, M.J.E and Blundell, T.L. The preparation of heavy atom derivatives of protein crystals for use in multiple isomorphous replacement. International Tables for Crystallography, Volume F Chapter 12.1. (2000)

Background

1979: B.Sc.(Hons) Biophysics, King's College London, University of London

1980-1984: Research Assistant/Ph.D. Cancer Research Campaign Unit, Department of Biophysics (now called The Randell Institute) 26-29 Drury Lane, King's College London, University of London

    Ph.D title:"Computer Aided Molecular Modelling of DNA-Drug Interactions"
    o Delevopement of molecular graphics/mechanics software
    o X-ray crystallographic analysis of drugs/dna fragments
    __Anthracyclines, Benzopyrenes, Dinuceotides,Drug-Dinucleotide complexes
    o Modelling drugs-dna interactions
    Computer System Managment of PDP 11/34(including diffractometer)

1984-1985 Continuation of the above work, but at the Cancer Research Campaign Unit Royal Marsden Hospital, Sutton, surrey

1985-1988 Post Doctorial Research Fellow with Professor Michael Sternberg at the Department of Crystallography (headed by Professor Tom Blundell), Birkbeck College University of London working on the following project:

    Protein Engineering: Prediction of Protein Structure from Sequence using Data Bases and Computer Graphics

Main project was the development of a Protein Structure Database using the Relational model (using ORACLE). Also responsible for computer management of VAX 11/750. This project was sponsored by SERC, ICI, GLAXO, RTZ, CELLTECH. Also in collaboration with Leeds University.

1988-2001 Chief Scientific Officer - Biomolecular Modelling Laboratory Imperial Cancer Research Fund, Lincoln's Inns Fields, London. Main role was systems administrator for group (Silicon Graphics workstations, Sun and IBM R6000 systems) and research and development of molecular graphics software, protein structure analysis.

2001- Structural Bioinformatics Group, Imperial College London

Publications

Islam,S.A.,Mason,A.,Neidle,S and Subbiah,A. (1981). Molecular structure of three hydroxyl derivatives of the hepatic carcinogen acetylaminofluorene. Evidence for a preferred orientation of the acetylamino side-chain. Carcinogenesis, volume 2 number 9,901-901.

Islam,S.A.,Neidle,S. and Subbiah,A. (1983). Molecular modelling studies on the non-covalent intercalative interactions between DNA and the enantiomers of anti-benzo[a]pyrene 7,8-diol-9,10-epoxides. Carcinogenesis, volume 4 number 2,211-215.

Aggarwal,A.,Islam,S.A.,Kuroda,R. Neidle,S. and Sanderson,M.R. (1983). The structure of the ribodinucleoside monophosphate guanylyl-3',5'-cytidine as its ammonium salt. Acta Cryst. B39,98-104.

Aggarwal,A.,Islam,S.A.,Kuroda,R. and Neidle,S. (1983). Drug-nucleic acid interactions: Proflavin intercalation into double-helical fragments of RNA and DNA. In Nucleic Acids: The Vectors of Life,495-509. B.Pullman and J.Jortner (eds). D.Reidle publishing company.

Aggarwal,A.,Islam,S.A. and Neidle,S. (1983). Computer modelling studies of the covalent interactions between DNA and the enantiomers of anti-7,8-diol,9,10-epoxy-benzo[a]pyrene. J. of Biomolecular Structure and Dynamics, 1.

Islam,S.A. and Neidle,S. (1983). Nucleic acid binding drugs. VII. Molecular-mechanics studies on the conformational properties of the anti-cancer drug daunomycin: some observations on the use of differing potential-energy functions. Acta Cryst. B39,114-119.

Almond,P.,Cutbush,S.D.,Islam,S.A.,Kuroda,R. and Neidle,S. (1983). Nucleic acid binding drugs. VIII. Structures of 1-[2-(diethylamino)ethylamino]anthracene-9,10-dione and 1,5-bis[2-(diethylamino)ethylamino]anthracene-9,10-dione. Models for anti-tumour drugs. Acta Cryst. C39,627-630.

Islam,S.A.,Neidle,S.,Gandecha,B.M. and Brown,J.R. (1983). Experimental and computer graphics simulation analysis of the DNA interactions of 1,8-bis-(2-diethylaminoethylamino)-anthracene-9,10-dione. A compound modelled on Doxorubicin. Biochemical Pharmocology, volume 32 number 18,2801-2808.

Islam,S.A.,Kuroda,R.,Neidle,S.,Brown,J.R.,Patterson,L.H. and Gandecha,B.M. (1983). Computer graphics in rational anti-cancer drug design. Communications,600th meeting of the biochemical society,Oxford,volume 10,501.

Aggarwal,A.,Islam,S.A.,Kuroda,R. and Neidle,S. (1984). X-ray crystallographic analysis of a ternary intercalation complex between proflavin and the dinucleoside monophosphates CpA and UpG. Biopolymers 23,1025-1041.

Islam,S.A. and Neidle S. (1984). Nucleic acid binding drugs. X. A theoretical study of proflavin intercalation into RNA and DNA fragments: Comparison with crystallographic results. Acta Cryst. B40,424-429.

Islam,S.A.,Neidle,S.,Partridge,M.,Patterson,L.H. and Brown,J.R. (1985). Comparative computer graphics and solution studies of the DNA interaction of substituted anthraquinones based on doxorubicin and mitoxantrone. J.Med.Chem. 28,857-864.

Islam, Suhail A., Ph.D. Thesis (1986), Computer Aided Molecular Modelling of Drug-Nucleic Acid Interactions. University of London.

Neidle,S.,Abraham,Z.H.L.,Collier,D.A. and Islam,S.A. (1987). Application of computer-assisted modelling to structure-activity studies with intercalating drugs. New avenues in developmental cancer chemotherapy. Chapter 4,83-109. Academic press.

McGregor, M.J., Islam, S.A. and Sternberg, M.J.E. (1987). Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 198, 295-310.

Akrigg, D., Bleasby, A.J., Dix, N.I.M., Findlay, J.B.C., North, A.C.T., Parry, S.D., Wootton, J.C., Bludell, T.L., Gardner, S.P., Hayes, F., Islam, S.A., Sternberg, M.J.E., Thornton, J.M. and Tickle, I.J. (1988). A protein sequence / structure database. Nature (London) 335, 745-746.

Blundell, T.L., Elliott, G., Gardener, S.P., Hubbard, T., Islam, S., Johnson, M., Mantafounis, D., Murray, R.P., Overington, J., Pitts, J.E., Sali, A., Sibanda, B.L., Singh, J., Sternberg, M.J.E., Sutcliffe, M.J., Thornton, J.M. and Travers, P. (1989). Protein engineering and design. Phil Trans R Soc Lond B 324, 447-460.

Islam, S.A. and Sternberg, M.J.E. (1989). A relational database of protein structure designed for flexible enquiries about conformation. Prot Eng 2, 431-442.

Bryant,S.H.,Islam,S.A. and Weaver,D.L. (1989). The surface area of monomeric proteins: Significance of power law behavior. Proteins 6,418-423.

Bates, P.A., McGregor, M.J., Islam, S.A., Sattentau, Q.J. and Sternberg, M.J.E. (1989). A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen. Prot Eng 3, 13-21.

Sternberg, M.J.E., Barton, G.J., Islam, S.A., McGregor, M.J. and Zvelebil, M.J.J.M. (1989). Modelling the structure and function of proteins from their amino acid sequence using databases. Computer-Aided Molecular Design, Chapter 13, 157-164. Ed. W. Richards.Ibc Technical Services Ltd,London.

Sternberg, M.J.E. and Islam, S.A. (1989). A relational database of protein structure. Biochemical Society Transactions 17, 845-847.

Islam, S.A., Sternberg, M.J.E. and Weaver, D.L. (1990). Bad contacts in protein structures. In Accuracy and reliability of macromolecular crystal structures, Henrick, K., Moss, D.S. and Tickle, I.J., eds. (Science and Engineering Research Council, Daresbury Laboratory, Warrington) pp. 53-62.

Islam, S.A. and Weaver, D.L. (1990). Molecular interactions in protein crystals: solvent accessible surface and stability. Proteins 8, 1-5.

McGregor, M.J., Bates, P.A., Islam, S.A., Sternberg, M.J.E. and Sattentau, Q.J. (1990). A predicted three-dimensional structure of CD4 and the location of the HIV gp120 binding region. In Protein Engineering - Protein Design in Basic Research, Medicine, and Industry, M.Ikehara, T.Oshima and K.Titani, eds. (Japan Scientific Societies Press, Tokyo) pp. 83-85.

Sternberg, M.J.E. and Islam, S.A. (1990). Local protein sequence similarity does not imply a structural relationship. Prot. Eng. 4, 125-131.

Carvin, D.C., Islam, S.A., Sternberg, M.J.E. and Blundell, T.B.L.. (1991). Establishment of A Heavy-Atom Databank, Henrick, K., Moss, D.S. and Tickle, I.J., eds. (Science and Engineering Research Council, Daresbury Laboratory, Warrington).

Islam, S.A. and Weaver, D.L. (1991). Variation of folded polypeptide surface area with probe size. Proteins 10, 300-314.

Islam,S.A.,Wolf,C.R.,Lennard,M.S. and Sternberg,M.J.E. (1991). A three-dimensional molecular template for substrates of human cytochrome P450 2D6 - Identification of the activation pathway of carcinogens and pharmaceuticals. Carcinogensis, Volume 12, Number 12, 2212-2219.

Sternberg, M.J.E. and Islam, S.A. (1991). Protein Sequences - Homologies and Motifs. TIBTECH. September 1991, Volume 9, 300-302. Elsevier Science Publishers (UK).

Bates, P.A., Islam , S.A. and Sternberg, M.J.E. Structures of Debrisquine Sulfate. Acta Cryst (1993) C49, pp 300-303

Islam, S.A., Weaver D.L. and Weaver T.D. (1994). MacMolecular: A Program for Visualization of Molecular Structures on the Macintosh. J. Mol. Graphics, (1994) vol 12, September , pp 231-234

Islam , S.A., Luo, J. and Sternberg, M.J.E. Identification and analysis of domains in proteins. Protein Engineering (1995) vol 8 no 6 pp 513-525

Sternberg, M.J.E., Hegyi, H., Islam, S.A., Luo, J., Russell, R.B., Towards an Intellegent System for the Automatic Assignment of Domains in Globular Proteins. In "ISMB-95 Proceedings Third International Conference on Intelligent Systems For Molecular Biology" Eds. C. Rawlings et al. pp 376-383, 1995. AAAI Press, Menlo Park, California

Lally, J.L., Newman, R.H., Knowles, P.P., Islam S.A., Coffer, A.I., Parker, M., and Freemont, P.S Crystallisation of an intact GST-Estrogen receptor hormone binding domain fusion protein (1998) Acta. Cryst. Section D., Vol D54 Part 3 423-426

Carivn, D, Islam, S.A., Sternberg, M.J.E. and Blundell, T.L. HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: A Resourse for Use in Multiple Isomorphous Replacement and Anomalous Scattering. Acta. Cryst. (1998). D54, 1199-1206

Carvin, D, Islam, S.A., Sternberg, M.J.E and Blundell, T.L. The preparation of heavy atom derivatives of protein crystals for use in multiple isomorphous replacement. International Tables for Crystallography, Volume F Chapter 12.1. (2000)

C. Shiels, S.A. Islam, R. Vatcheva, P. Sasieni, M. J. E. Sternberg, D. Sheer and P.S. Freemont. PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J. Cell Sci. 114: 3705-3716 (2001)

Suhail A. Islam, Martin Karplus, David L. Weaver Application of the Diffusion-Collision Model to the Folding of Three-helix Bundle Proteins J. Mol. Biol. 318, 199-215 (2002)

B Jones, E L Jones, S A Bonney, H N Patel, A R Mensenkamp, S Eichenbaum-Voline, M Rudling, U Myrdal, G Annesi, S Naik, N Meadows, A Quattrone, S A Islam, R P Naoumova, B Angelin, R Infante, E Levy, C C Roy, P S Freemont, J Scott & C C Shoulders Mutations in a Sar1 GTPase of COPII vesicles are associated with lipid absorption disorders. Nature Genetics 2003 Vol 34, 29-31

D.J. Cousins, S.A. Islam, M.R. Sanderson, Y.G. Proykova, C. Crane-Robinson and D.Z. Staynov Redefinition of the Cleavage Sites of DNase I on the Nucleosome Core Particle. J. Mol. Biol. (2004) 335, 1199-1211.

Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions Wang J, Shiels C, Sasieni P, Wu PJ, Islam SA, Freemont PS, Sheer D J CELL BIOL 164(4) 16 Feb 2004

Islam, S.A., Karplus,M., Weaver, D.L. The Role of Sequence and Structure in Protein Folding Kinetics: the Diffusion-Collision Model Applied to Proteins L and G. Structure 2004 Vol 12(10), 1823-1832

Protein-protein docking using 3D-dock in rounds 3, 4, and 5 of CAPRI Carter P, Lesk VI, Islam SA, Sternberg MJE PROTEINS 60(2) 01 Aug 2005

The proteome: structure, function and evolution. Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ Philos Trans R Soc Lond B Biol Sci 361(1467) 29 Mar 2006

The transcriptional regulator CBP has defined spatial associations within interphase nuclei. McManus KJ, Stephens DA, Adams NM, Islam SA, Freemont PS, Hendzel MJ PLoS Comput Biol 2(10) 20 Oct 2006

Quantitative analysis of cell nucleus organisation. Shiels C, Adams NM, Islam SA, Stephens DA, Freemont PS PLoS Comput Biol 3(7) Jul 2007


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