RSTB_361_1467.qxp 2/16/06 7:59 PM Page 1 Philosophical Transactions of The Royal Society B ISSN 0962-8436

volume 361

29 March 2006 number 1467 volume 361 . number 1467 . pages 387–527

pages 387–527 Bioinformatics: from molecules to systems

Papers of a Discussion Meeting organised and edited by David Jones, In this issue Michael Sternberg and Janet Thornton Bioinformatics: from molecules to systems Introduction. Bioinformatics: from molecules to systems 389 D. T. Jones, M. J. E. Sternberg & J. M. Thornton Papers of a Discussion Meeting organised and edited by David Jones, Michael Sternberg and Janet Thornton Finding the molecular basis of complex genetic variation in humans and mice 393 R. Mott Comparative genomics and genome evolution in yeasts 403 K. H. Wolfe Structural biology and bioinformatics in drug design: opportunities and challenges

for target identification and lead discovery 413 volume 361 T. L. Blundell, B. L. Sibanda, R. W. Montalvão, S. Brewerton, V. Chelliah, C. L. Worth, N. J. Harmer, O. Davies & D. Burke Exploiting protein structure data to explore the evolution of protein function and biological complexity 425 R. L. Marsden, J. A. G. Ranea, A. Sillero, O. Redfern, C. Yeats, M. Maibaum, D. Lee, S. Addou, G. A. Reeves, T. J. Dallman & C. A. Orengo .

The proteome: structure, function and evolution 441 number 1467 K. Fleming, L. A. Kelley, S. A. Islam, R. M. MacCallum, A. Muller, F. Pazos & M. J. E. Sternberg Rigorous performance evaluation in protein structure modelling and implications for computational biology 453 J. Moult Prediction and design of macromolecular structures and interactions 459 D. Baker .

Towards genome-scale structure prediction for transmembrane proteins 465 pages 387–527 N. Hurwitz, M. Pellegrini-Calace & D. T. Jones From genomes to systems: the path with yeast 477 S. G. Oliver Modelling in molecular biology: describing transcription regulatory networks at different scales 483 T. Schlitt & A. Brazma

Transcriptional noise and cellular heterogeneity in mammalian macrophages 495 . S. Ramsey, A. Ozinsky, A. Clark, K. D. Smith, P. de Atauri, V. Thorsson, D. Orrell & H. Bolouri 29 March 2006 The origins and evolution of functional modules: lessons from protein complexes 507 J. B. Pereira-Leal, E. D. Levy & S. A. Teichmann Comparative analysis of environmental sequences: potential and challenges 519 K. U. Foerstner, C. von Mering & P. Bork Bioinformatic challenges for the next decade(s) 525 D. Eisenberg, E. Marcotte, A. D. McLachlan & M. Pellegrini

The world’s longest running international science journal Founded in 1660, the Royal Society is the independent scientific academy of the UK, dedicated to promoting excellence in science www.journals.royalsoc.ac.uk Registered Charity No 207043 Published in Great Britain by The Royal Society, 29 March 2006 6–9 Carlton House Terrace, London SW1Y 5AG