Protein structure prediction.

Genome sequencing projects continue to provide a flood of new protein sequences, and prediction methods remain an important means of adding structural information. Recently, there have been advances in secondary structure prediction, which feed, in turn, into improved fold recognition algorithms. Finally, there have been technical improvements in comparative modelling, and studies of the expected accuracy of three-dimensional structural models built by this method.

[1]  R Sánchez,et al.  Advances in comparative protein-structure modelling. , 1997, Current opinion in structural biology.

[2]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[3]  Ram Samudrala,et al.  Ab initio protein structure prediction using a combined hierarchical approach , 1999, Proteins.

[4]  G. Barton,et al.  Protein fold recognition by mapping predicted secondary structures. , 1996, Journal of molecular biology.

[5]  T. Blundell,et al.  Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. , 1997, Journal of molecular biology.

[6]  J. Greer,et al.  Comparative modeling of homologous proteins. , 1991, Methods in enzymology.

[7]  Eytan Domany,et al.  Protein fold recognition and dynamics in the space of contact maps , 1996, Proteins.

[8]  J. Wójcik,et al.  New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. , 1999, Journal of molecular biology.

[9]  M. Sternberg,et al.  Benchmarking PSI-BLAST in genome annotation. , 1999, Journal of molecular biology.

[10]  D. Haussler,et al.  Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.

[11]  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.

[12]  S Sunyaev,et al.  Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing. , 1997, Protein engineering.

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

[14]  A G Murzin,et al.  Distant homology recognition using structural classification of proteins , 1997, Proteins.

[15]  A A Salamov,et al.  Protein secondary structure prediction using local alignments. , 1997, Journal of molecular biology.

[16]  R. Samudrala,et al.  Determinants of side chain conformational preferences in protein structures. , 1998, Protein engineering.

[17]  Roland L. Dunbrack,et al.  Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.

[18]  T Kawabata,et al.  Improvement of protein secondary structure prediction using binary word encoding , 1997, Proteins.

[19]  M C Peitsch,et al.  ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. , 1996, Biochemical Society transactions.

[20]  Roland L. Dunbrack,et al.  Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.

[21]  U. Lessel,et al.  Importance of anchor group positioning in protein loop prediction , 1999, Proteins.

[22]  Ram Samudrala,et al.  A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence , 1999, Pacific Symposium on Biocomputing.

[23]  Richard H. Lee Protein model building using structural homology , 1992, Nature.

[24]  J. M. Levin,et al.  Exploring the limits of nearest neighbour secondary structure prediction. , 1997, Protein engineering.

[25]  D J Kyle,et al.  Accuracy and reliability of the scaling‐relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational samplings , 1996, Proteins.

[26]  W R Taylor,et al.  Distance geometry based comparative modelling. , 1997, Folding & design.

[27]  Roland L. Dunbrack,et al.  Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. , 1997, Journal of molecular biology.

[28]  S Vajda,et al.  Selecting near‐native conformations in homology modeling: The role of molecular mechanics and solvation terms , 1998, Protein science : a publication of the Protein Society.

[29]  P. Munson,et al.  Statistical significance of hierarchical multi‐body potentials based on Delaunay tessellation and their application in sequence‐structure alignment , 1997, Protein science : a publication of the Protein Society.

[30]  R. M. Abarbanel,et al.  Turn prediction in proteins using a pattern-matching approach. , 1986, Biochemistry.

[31]  E. Koonin,et al.  Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. , 1999, Journal of molecular biology.

[32]  H. Umeyama,et al.  Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms. , 1997, Protein engineering.

[33]  Jan Hermans,et al.  Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model , 1998, Proteins.

[34]  C. Chothia,et al.  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[35]  J. Mendes,et al.  Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. , 1999, Biopolymers.

[36]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[37]  T. L. Blundell,et al.  Knowledge-based prediction of protein structures and the design of novel molecules , 1987, Nature.

[38]  J. Garnier,et al.  Protein topology recognition from secondary structure sequences: application of the hidden Markov models to the alpha class proteins. , 1997, Journal of molecular biology.

[39]  T. Blundell,et al.  Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction , 1996, Protein science : a publication of the Protein Society.

[40]  David C. Jones,et al.  Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. , 1996, Journal of molecular biology.

[41]  J Moult,et al.  The current state of the art in protein structure prediction. , 1996, Current opinion in biotechnology.

[42]  M. Karplus,et al.  PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.

[43]  P. Koehl,et al.  Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. , 1994, Journal of molecular biology.

[44]  L Shapiro,et al.  The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. , 1998, Structure.

[45]  S. Bryant Evaluation of threading specificity and accuracy , 1996, Proteins.

[46]  Andrew J. Martin,et al.  Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. , 1996, Journal of molecular biology.

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

[48]  S. L. Mayo,et al.  Probing the role of packing specificity in protein design. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[49]  E S Huang,et al.  Factors affecting the ability of energy functions to discriminate correct from incorrect folds. , 1997, Journal of molecular biology.

[50]  W. Taylor,et al.  Multiple sequence threading: an analysis of alignment quality and stability. , 1997, Journal of molecular biology.

[51]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[52]  E. Huang,et al.  Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. , 1999, Journal of molecular biology.

[53]  A. Finkelstein,et al.  Residue-residue mean-force potentials for protein structure recognition. , 1997, Protein engineering.

[54]  C Bystroff,et al.  Blind predictions of local protein structure in CASP2 targets using the I‐sites library , 1997, Proteins.

[55]  B. Lee Relation between volume correction and the standard state. , 1994, Biophysical chemistry.

[56]  L. Mirny,et al.  Protein structure prediction by threading. Why it works and why it does not. , 1998, Journal of molecular biology.

[57]  M. Sternberg,et al.  Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. , 1997, Journal of molecular biology.

[58]  F. Cohen,et al.  Multiple sequence information for threading algorithms. , 1996, Journal of molecular biology.

[59]  B. Rost,et al.  Marrying structure and genomics. , 1998, Structure.

[60]  M J Sippl,et al.  Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.

[61]  P Argos,et al.  The future of protein secondary structure prediction accuracy. , 1997, Folding & design.

[62]  Improved method for prediction of protein backbone U‐turn positions and major secondary structural elements between U‐turns , 1997, Proteins.

[63]  P. Wolynes,et al.  Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment , 1996, Protein science : a publication of the Protein Society.

[64]  G T Montelione,et al.  Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three‐dimensional structure of murine homeodomain Msx‐1 , 1997, Protein science : a publication of the Protein Society.

[65]  Anders Krogh,et al.  Improving Predicition of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments , 1996, J. Comput. Biol..

[66]  Manuel C. Peitsch,et al.  Protein Modeling by E-mail , 1995, Bio/Technology.

[67]  K. Fidelis,et al.  Comparison of systematic search and database methods for constructing segments of protein structure. , 1994, Protein engineering.

[68]  D. T. Jones,et al.  Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure , 1999, Proteins.

[69]  P. Argos,et al.  Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. , 1996, Protein engineering.

[70]  B. Honig,et al.  Evaluation of the conformational free energies of loops in proteins , 1994, Proteins.

[71]  R A Friesner,et al.  Prediction of loop geometries using a generalized born model of solvation effects , 1999, Proteins.

[72]  L Rychlewski,et al.  Secondary structure prediction using segment similarity. , 1997, Protein engineering.

[73]  C. Bystroff,et al.  Three‐dimensional structures and contexts associated with recurrent amino acid sequence patterns , 1997, Protein science : a publication of the Protein Society.

[74]  A. Godzik,et al.  Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. , 1997, Folding & design.

[75]  R. Samudrala,et al.  An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.

[76]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[77]  D. Shortle Protein fold recognition , 1995, Nature Structural Biology.

[78]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[79]  I Lasters,et al.  All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination. , 1997, Folding & design.

[80]  P Tufféry,et al.  Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space. , 1997, Protein engineering.

[81]  U. Lessel,et al.  Creation and characterization of a new, non-redundant fragment data bank. , 1997, Protein engineering.

[82]  W R Taylor,et al.  Homology modelling by distance geometry. , 1996, Folding & design.

[83]  Masahiro Ito,et al.  Prediction of protein secondary structure using the 3D-1D compatibility algorithm , 1997, Comput. Appl. Biosci..

[84]  M. Levitt,et al.  Accuracy of side‐chain prediction upon near‐native protein backbones generated by ab initio folding methods , 1998, Proteins.

[85]  Baldomero Oliva,et al.  An automated classification of the structure of protein loops. , 1997, Journal of molecular biology.

[86]  Ying Xu,et al.  A polynomial-time algorithm for a class of protein threading problems , 1996, Comput. Appl. Biosci..

[87]  M. Totrov,et al.  Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. , 1997, Journal of molecular biology.

[88]  B. Rost,et al.  Protein fold recognition by prediction-based threading. , 1997, Journal of molecular biology.

[89]  R. King,et al.  Identification and application of the concepts important for accurate and reliable protein secondary structure prediction , 1996, Protein science : a publication of the Protein Society.

[90]  L. Lai,et al.  Protein loops on structurally similar scaffolds: database and conformational analysis. , 1999, Biopolymers.

[91]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

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

[93]  T. Huber,et al.  Protein fold recognition without Boltzmann statistics or explicit physical basis , 1998, Protein science : a publication of the Protein Society.

[94]  M. Karplus,et al.  Discrimination of the native from misfolded protein models with an energy function including implicit solvation. , 1999, Journal of molecular biology.

[95]  N N Alexandrov,et al.  Alignment algorithm for homology modeling and threading , 1998, Protein science : a publication of the Protein Society.

[96]  A. Liwo,et al.  Calculation of protein conformation by global optimization of a potential energy function , 1999, Proteins.

[97]  E. Lindahl,et al.  Identification of related proteins on family, superfamily and fold level. , 2000, Journal of molecular biology.

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

[99]  S Subbiah,et al.  A structural explanation for the twilight zone of protein sequence homology. , 1996, Structure.

[100]  R A Goldstein,et al.  Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information , 1997, Protein science : a publication of the Protein Society.

[101]  T. Blundell,et al.  Knowledge-based protein modeling. , 1994, Critical reviews in biochemistry and molecular biology.

[102]  T L Blundell,et al.  The use of amino acid patterns of classified helices and strands in secondary structure prediction. , 1996, Journal of molecular biology.

[103]  B. Rost Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[104]  D B Gordon,et al.  Branch-and-terminate: a combinatorial optimization algorithm for protein design. , 1999, Structure.

[105]  Gordon M. Crippen Failures of inverse folding and threading with gapped alignment , 1996 .

[106]  D Eisenberg,et al.  A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. , 1997, Journal of molecular biology.