Recent developments in computational proteomics.

The mapping of the human genome was completed earlier this year and efforts are underway to understand the role of gene products (i.e. proteins) in biological pathways and human disease and to exploit their functional roles to derive protein therapeutics and protein-based drugs. A key component to the next revolution in the 'post-genomic' era will be the increasingly widespread use of protein structure in rational experimental design. Improvements in quality, availability and utility of large-scale 3D and 4D protein structural information are enabling a revolution in rational design, having particular impact on drug discovery and optimization. New computational methodologies now yield modeled structures that are, in many cases, quantitatively comparable with crystal structures, at a fraction of the cost.

[1]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[2]  Udo Heinemann,et al.  Structural genomics in Europe: Slow start, strong finish? , 2000, Nature Structural Biology.

[3]  Leo S. D. Caves,et al.  MBO(N)D: A multibody method for long-time molecular dynamics simulations , 2000, J. Comput. Chem..

[4]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[5]  J. Ponder,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions , 1998 .

[6]  J. Skolnick,et al.  From genes to protein structure and function: novel applications of computational approaches in the genomic era. , 2000, Trends in biotechnology.

[7]  Jakob Bohr,et al.  Protein folding and wring resonances. , 1997, Biophysical chemistry.

[8]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[9]  Christophe Geourjon,et al.  SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments , 1995, Comput. Appl. Biosci..

[10]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[11]  A. Panchenko,et al.  Threading with explicit models for evolutionary conservation of structure and sequence , 1999, Proteins.

[12]  R Abagyan,et al.  The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. , 1993, Structure.

[13]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[14]  Y. Matsuo,et al.  Structural genomics projects in Japan. , 2000, Progress in biophysics and molecular biology.

[15]  P. Argos,et al.  Seventy‐five percent accuracy in protein secondary structure prediction , 1997, Proteins.

[16]  Thomas C. Terwilliger,et al.  Structural genomics in North America , 2000, Nature Structural Biology.

[17]  G J Barton,et al.  Evaluation and improvement of multiple sequence methods for protein secondary structure prediction , 1999, Proteins.

[18]  M. Vásquez,et al.  Modeling side-chain conformation. , 1996, Current opinion in structural biology.

[19]  J M Chandonia,et al.  New methods for accurate prediction of protein secondary structure , 1999, Proteins.

[20]  Ab initio simulation of chemical shift effects from metal ion binding in Bacitracin A , 2000 .

[21]  S. Wodak,et al.  Protein structure prediction by threading methods: Evaluation of current techniques , 1995, Proteins.

[22]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[23]  John C. Norvell,et al.  Structural genomics programs at the US National Institute of General Medical Sciences , 2000, Nature Structural Biology.

[24]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[25]  P Argos,et al.  A method to configure protein side-chains from the main-chain trace in homology modelling. , 1993, Journal of molecular biology.

[26]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.