The current state of the art in protein structure prediction.

The capabilities of current protein structure prediction methods have been assessed from the outcome of a set of blind tests. In comparative modeling, many of the numerical methods did not perform as well as expected, although the resulting structures are still of great practical use. The new methods of fold identification ('threading') were partially successful, and show considerable promise for the future. Except for secondary structure data, results from traditional ab initio methods were poor. A second blind prediction experiment is underway, and progress in all areas is expected.

[1]  F E Cohen,et al.  Evaluation of current techniques for Ab initio protein structure prediction , 1995, Proteins.

[2]  S Subbiah,et al.  How similar must a template protein be for homology modeling by side-chain packing methods? , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[3]  G J Barton,et al.  Protein secondary structure prediction. , 1995, Current opinion in structural biology.

[4]  R J Read,et al.  Critical evaluation of comparative model building of Streptomyces griseus trypsin. , 1984, Biochemistry.

[5]  J. Cherfils,et al.  Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase , 1996, Nature Structural Biology.

[6]  M J Sippl,et al.  Progress in fold recognition , 1995, Proteins.

[7]  J. Moult,et al.  An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.

[8]  C. Sander,et al.  Challenging times for bioinformatics , 1995, Nature.

[9]  Harold A. Scheraga,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops , 1990 .

[10]  J. Moult,et al.  Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms , 1995, Proteins.

[11]  R. Lathrop.  The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.

[12]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures , 1987, Biopolymers.

[13]  K Mizuguchi,et al.  Seeking significance in three-dimensional protein structure comparisons. , 1995, Current opinion in structural biology.

[14]  C. Chothia.  One thousand families for the molecular biologist , 1992, Nature.

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

[16]  M. James,et al.  A critical assessment of comparative molecular modeling of tertiary structures of proteins * , 1995, Proteins.

[17]  F E Cohen,et al.  Structure-based inhibitor design by using protein models for the development of antiparasitic agents. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Ram Samudrala,et al.  Confronting the problem of interconnected structural changes in the comparative modeling of proteins , 1995, Proteins.

[19]  R. Srinivasan,et al.  LINUS: A hierarchic procedure to predict the fold of a protein , 1995, Proteins.

[20]  J. Greer.  Comparative modeling methods: Application to the family of the mammalian serine proteases , 1990, Proteins.

[21]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[22]  Dietlind L. Gerloff,et al.  The phospho‐β‐galactosidase and synaptotagmin predictions , 1995 .

[23]  M. Karplus,et al.  Evaluation of comparative protein modeling by MODELLER , 1995, Proteins.

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

[25]  T. Hubbard,et al.  Fold recognition and ab initio structure predictions using hidden markov models and β‐strand pair potentials , 1995, Proteins.

[26]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[27]  S. Bryant,et al.  Threading a database of protein cores , 1995, Proteins.

[28]  J. Risler,et al.  Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix. , 1988, Journal of molecular biology.

[29]  David C. Jones,et al.  Potential energy functions for threading. , 1996, Current opinion in structural biology.

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

[31]  J M Thornton,et al.  Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing , 1995, Proteins.

[32]  Eaton E. Lattman,et al.  Protein structure prediction: A special issue , 1995 .

[33]  B. Rost,et al.  Redefining the goals of protein secondary structure prediction. , 1994, Journal of molecular biology.

[34]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.