A Historical Perspective and Overview of Protein Structure Prediction

[1]  M. Baker,et al.  Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. , 2005, Journal of structural biology.

[2]  Z. Weng,et al.  Protein–protein docking benchmark 2.0: An update , 2005, Proteins.

[3]  Alexander V. Diemand,et al.  The Swiss‐Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants , 2004, Human mutation.

[4]  David Haussler,et al.  LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources , 2005, Bioinform..

[5]  Chris Sander,et al.  Completeness in structural genomics , 2001, Nature Structural Biology.

[6]  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.

[7]  Richard Bonneau,et al.  Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.

[8]  Kimmen Sjölander,et al.  COACH : profile-profile alignment of protein families using hidden Markov models , 2003 .

[9]  G. Heijne.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[10]  Andrej Sali,et al.  Combining electron microscopy and comparative protein structure modeling. , 2005, Current opinion in structural biology.

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

[12]  Adam Godzik,et al.  A method for predicting protein structure from sequence , 1993, Current Biology.

[13]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

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

[15]  David T. Jones,et al.  Rapid protein domain assignment from amino acid sequence using predicted secondary structure , 2002, Protein science : a publication of the Protein Society.

[16]  J. Skolnick,et al.  Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.

[17]  A J Cuticchia,et al.  TM Finder: A prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales , 2001, Protein science : a publication of the Protein Society.

[18]  Alexandre M J J Bonvin,et al.  Data‐driven docking for the study of biomolecular complexes , 2005, The FEBS journal.

[19]  Julian Lee,et al.  Protein structure prediction based on fragment assembly and parameter optimization. , 2005, Biophysical chemistry.

[20]  N. P. Todorov,et al.  Receptor flexibility in de novo ligand design and docking. , 2005, Journal of medicinal chemistry.

[21]  D. Phillips,et al.  A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. , 1969, Journal of molecular biology.

[22]  B Busetta,et al.  The prediction of protein domains. , 1984, Biochimica et biophysica acta.

[23]  R. Russell,et al.  Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. , 2004, Journal of molecular biology.

[24]  H A Scheraga,et al.  Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[27]  P. Carloni,et al.  Molecular modeling of ion channels: structural predictions. , 2003, Current opinion in chemical biology.

[28]  C Kooperberg,et al.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.

[29]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[30]  Marcin Feder,et al.  A “FRankenstein's monster” approach to comparative modeling: Merging the finest fragments of Fold‐Recognition models and iterative model refinement aided by 3D structure evaluation , 2003, Proteins.

[31]  K. Dill,et al.  Cooperativity in protein-folding kinetics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Dong Xu,et al.  Improving the performance of DomainParser for structural domain partition using neural network. , 2003, Nucleic acids research.

[33]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[34]  G. Heijne.  The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans‐membrane topology , 1986, The EMBO journal.

[35]  J. Skolnick,et al.  Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model , 1998, Proteins.

[36]  C. Sander,et al.  Parser for protein folding units , 1994, Proteins.

[37]  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.

[38]  B. Honig,et al.  Protein structure prediction: inroads to biology. , 2005, Molecular cell.

[39]  J. Skolnick,et al.  Monte carlo simulations of protein folding. I. Lattice model and interaction scheme , 1994, Proteins.

[40]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[41]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[42]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[43]  A. Krogh,et al.  Reliability measures for membrane protein topology prediction algorithms. , 2003, Journal of molecular biology.

[44]  H. Scheraga,et al.  Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Daniel Fischer,et al.  3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor , 2003, Proteins.

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

[47]  G J Barton,et al.  Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions , 1995, Protein science : a publication of the Protein Society.

[48]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[49]  G. von Heijne,et al.  Materials and Methods Figs. S1 to S3 References and Notes Global Topology Analysis of the Escherichia Coli Inner Membrane Proteome , 2022 .

[50]  Adam Godzik,et al.  Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins , 2005, Pacific Symposium on Biocomputing.

[51]  O. Schueler‐Furman,et al.  Progress in Modeling of Protein Structures and Interactions , 2005, Science.

[52]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.

[53]  Ying Xu,et al.  PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction , 2004, Nucleic Acids Res..

[54]  C. Anfinsen,et al.  The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Paul A. Bates,et al.  Domain Fishing: a first step in protein comparative modelling , 2002, Bioinform..

[56]  A. Sali,et al.  Alignment of protein sequences by their profiles , 2004, Protein science : a publication of the Protein Society.

[57]  Jeffrey J. Gray,et al.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.

[58]  C. Anfinsen,et al.  Studies on the gross structure, cross-linkages, and terminal sequences in ribonuclease. , 1954, The Journal of biological chemistry.

[59]  C. Hogue,et al.  Armadillo: domain boundary prediction by amino acid composition. , 2005, Journal of molecular biology.

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

[61]  Arieh Warshel,et al.  Bicycle-pedal model for the first step in the vision process , 1976, Nature.

[62]  G. Tusnády,et al.  Principles governing amino acid composition of integral membrane proteins: application to topology prediction. , 1998, Journal of molecular biology.

[63]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[64]  C. Deane,et al.  CODA: A combined algorithm for predicting the structurally variable regions of protein models , 2001, Protein science : a publication of the Protein Society.

[65]  S. White.  The progress of membrane protein structure determination , 2004, Protein science : a publication of the Protein Society.

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

[67]  Anders Liljas,et al.  Recognition of structural domains in globular proteins , 1974 .

[68]  Marc Baaden,et al.  A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA. , 2003, Journal of molecular biology.

[69]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[70]  Hongyi Zhou,et al.  Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments , 2004, Proteins.

[71]  Golan Yona,et al.  Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. , 2002, Journal of molecular biology.

[72]  D. Baker,et al.  Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins , 1999, Proteins.

[73]  A Keith Dunker,et al.  Combining prediction, computation and experiment for the characterization of protein disorder. , 2004, Current opinion in structural biology.

[74]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[75]  J. Skolnick,et al.  Reduced models of proteins and their applications , 2004 .

[76]  A. Watts,et al.  Computational analysis of mutations in the transmembrane region of Vpu from HIV-1. , 2005, Biochimica et biophysica acta.

[77]  Johan Desmet,et al.  The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.

[78]  T S Baker,et al.  Low resolution meets high: towards a resolution continuum from cells to atoms. , 1996, Current opinion in structural biology.

[79]  Martin Vingron,et al.  Increase of functional diversity by alternative splicing. , 2003, Trends in genetics : TIG.

[80]  Arne Elofsson,et al.  Structure prediction meta server , 2001, Bioinform..

[81]  B. Rost,et al.  Transmembrane helices predicted at 95% accuracy , 1995, Protein science : a publication of the Protein Society.

[82]  M C Peitsch,et al.  A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors. , 1993, International immunology.

[83]  A. Liwo,et al.  Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Marc A. Martí-Renom,et al.  EVA: evaluation of protein structure prediction servers , 2003, Nucleic Acids Res..

[85]  O. Schueler‐Furman,et al.  Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility , 2005, Proteins.

[86]  T. Blundell,et al.  Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.

[87]  Ruth Nussinov,et al.  Protein structure prediction via combinatorial assembly of sub-structural units , 2003, ISMB.

[88]  J. Skolnick,et al.  TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[89]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[90]  J. Greer.  Comparative model-building of the mammalian serine proteases. , 1981, Journal of molecular biology.

[91]  David C. Jones,et al.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.

[92]  A. Godzik,et al.  The interplay of fold recognition and experimental structure determination in structural genomics. , 2004, Current opinion in structural biology.

[93]  M. Baker,et al.  Electron cryomicroscopy of biological machines at subnanometer resolution. , 2005, Structure.

[94]  Narayanan Eswar,et al.  MODBASE, a database of annotated comparative protein structure models , 2002, Nucleic Acids Res..

[95]  Adrian A Canutescu,et al.  Access the most recent version at doi: 10.1110/ps.03154503 References , 2003 .

[96]  Francesca Fanelli,et al.  Computational modeling approaches to structure-function analysis of G protein-coupled receptors. , 2005, Chemical reviews.

[97]  M. Levitt,et al.  Refinement of protein conformations using a macromolecular energy minimization procedure. , 1969, Journal of molecular biology.

[98]  F. Sanger,et al.  The amide groups of insulin. , 1955, The Biochemical journal.

[99]  Gerhard Wagner,et al.  TreeDock: a tool for protein docking based on minimizing van der Waals energies. , 2002, Journal of the American Chemical Society.

[100]  J. Skolnick.  Monte Carlo Simulations of Protein Folding , 2003 .

[101]  H. Berendsen,et al.  COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .

[102]  John Moult,et al.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. , 2005, Current opinion in structural biology.

[103]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[104]  H A Scheraga,et al.  Minimization of polypeptide energy. II. Preliminary structures of oxytocin, vasopressin, and an octapeptide from ribonuclease. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[105]  C. Levinthal.  Are there pathways for protein folding , 1968 .

[106]  Lee.  Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala98-->Val mutants of T4 lysozyme. , 1995, Folding & design.

[107]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[108]  Arne Elofsson,et al.  3D-Jury: A Simple Approach to Improve Protein Structure Predictions , 2003, Bioinform..

[109]  D. Baker,et al.  Prediction of local structure in proteins using a library of sequence-structure motifs. , 1998, Journal of molecular biology.

[110]  Arieh Warshel,et al.  Molecular dynamics simulations of biological reactions. , 2002, Accounts of chemical research.

[111]  R. Nussinov,et al.  A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.

[112]  M. Saier,et al.  The β‐barrel finder (BBF) program, allowing identification of outer membrane β‐barrel proteins encoded within prokaryotic genomes , 2002 .

[113]  Xiaojun Guan,et al.  Domain Identification by Clustering Sequence Alignments , 1997, ISMB.

[114]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[115]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[116]  Ingvar Eidhammer,et al.  BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of Gram-negative bacteria , 2004, Nucleic Acids Res..

[117]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[118]  Ivan Rayment,et al.  Three-dimensional atomic model of F-actin decorated with Dictyostelium myosin S1 , 1993, Nature.

[119]  José D Faraldo-Gómez,et al.  OmpA: a pore or not a pore? Simulation and modeling studies. , 2002, Biophysical journal.

[120]  P. Bork,et al.  Structure-Based Assembly of Protein Complexes in Yeast , 2004, Science.

[121]  David Baker,et al.  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[122]  G M Clore,et al.  Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[123]  Peter A. Kollman,et al.  Computational alanine scanning of the 1:1 human growth hormone–receptor complex , 2002, J. Comput. Chem..

[124]  C. Lee,et al.  Predicting protein mutant energetics by self-consistent ensemble optimization. , 1994, Journal of molecular biology.

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

[126]  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.

[127]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[128]  S. Sudarsanam,et al.  Modeling protein loops using a ϕi+1, Ψi dimer database , 1995, Protein science : a publication of the Protein Society.

[129]  G M Crippen,et al.  Minimization of polypeptide energy. X. A global search algorithm. , 1971, Archives of biochemistry and biophysics.

[130]  Stephen H. Bryant,et al.  Domain size distributions can predict domain boundaries , 2000, Bioinform..

[131]  R A Goldstein,et al.  Models of natural mutations including site heterogeneity , 1998, Proteins.

[132]  J Lundström,et al.  Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.

[133]  P. Koehl,et al.  A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling , 1995, Nature Structural Biology.

[134]  B. Rost,et al.  State-of-the-art in membrane protein prediction. , 2002, Applied bioinformatics.

[135]  Lei Xie,et al.  Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling , 2003, Proteins.

[136]  S. Bryant,et al.  An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.

[137]  K. Schulten,et al.  Self-organizing neural networks bridge the biomolecular resolution gap. , 1998, Journal of molecular biology.

[138]  Peter A. Kollman,et al.  AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .

[139]  M J Sippl,et al.  Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. , 1992, Journal of molecular biology.

[140]  R Nussinov,et al.  Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

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

[142]  M B Swindells,et al.  A procedure for detecting structural domains in proteins , 1995, Protein science : a publication of the Protein Society.

[143]  George D. Rose,et al.  Prediction of chain turns in globular proteins on a hydrophobic basis , 1978, Nature.

[144]  Janusz M. Bujnicki,et al.  GeneSilico protein structure prediction meta-server , 2003, Nucleic Acids Res..

[145]  Daniel J Rigden,et al.  Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. , 2002, Protein engineering.

[146]  C DeLisi,et al.  The detection and classification of membrane-spanning proteins. , 1985, Biochimica et biophysica acta.

[147]  O. Galzitskaya,et al.  Prediction of protein domain boundaries from sequence alone , 2003, Protein science : a publication of the Protein Society.

[148]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[149]  A. Roseman.  Docking structures of domains into maps from cryo-electron microscopy using local correlation. , 2000, Acta crystallographica. Section D, Biological crystallography.

[150]  Nick V Grishin,et al.  Access the most recent version at doi: 10.1110/ps.03197403 References , 2003 .

[151]  M. Sternberg,et al.  Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.

[152]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[153]  I. Simon,et al.  A possible way for prediction of domain boundaries in globular proteins from amino acid sequence. , 1986, Biochemical and biophysical research communications.

[154]  Jun S. Liu,et al.  Gibbs motif sampling: Detection of bacterial outer membrane protein repeats , 1995, Protein science : a publication of the Protein Society.

[155]  M. Baker,et al.  Bridging the information gap: computational tools for intermediate resolution structure interpretation. , 2001, Journal of molecular biology.

[156]  A Elofsson,et al.  Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. , 1997, Protein engineering.

[157]  D Xu,et al.  Model for the three‐dimensional structure of vitronectin: Predictions for the multi‐domain protein from threading and docking , 2001, Proteins.

[158]  Ying Xu,et al.  Raptor: Optimal Protein Threading by Linear Programming , 2003, J. Bioinform. Comput. Biol..

[159]  R. A. George,et al.  Protein domain identification and improved sequence similarity searching using PSI‐BLAST , 2002, Proteins.

[160]  B. Bush,et al.  Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[161]  Zhiping Weng,et al.  ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5 , 2005, Proteins.

[162]  M. Sippl.  Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.

[163]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[164]  D. Wetlaufer.  Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[165]  Y Xu,et al.  Protein threading using PROSPECT: Design and evaluation , 2000, Proteins.

[166]  M. Ubbink,et al.  The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. , 1998, Structure.

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

[168]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[169]  Eleanor J. Gardiner,et al.  Protein docking using a genetic algorithm , 2001, Proteins.

[170]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[171]  Zhiping Weng,et al.  A protein–protein docking benchmark , 2003, Proteins.

[172]  S. Brenner.  A tour of structural genomics , 2001, Nature Reviews Genetics.

[173]  A. Godzik,et al.  Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.

[174]  Wen Jiang,et al.  Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches. , 2002, Current opinion in structural biology.

[175]  A. Liwo,et al.  Protein structure prediction by global optimization of a potential energy function. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[176]  D T Jones,et al.  Prediction of novel and analogous folds using fragment assembly and fold recognition , 2005, Proteins.

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

[178]  I. Vakser.  Protein docking for low-resolution structures. , 1995, Protein engineering.

[179]  D. Baker,et al.  Prospects for ab initio protein structural genomics. , 2001, Journal of molecular biology.

[180]  K. Misura,et al.  PROTEINS: Structure, Function, and Bioinformatics 59:15–29 (2005) Progress and Challenges in High-Resolution Refinement of Protein Structure Models , 2022 .

[181]  Harpreet Kaur,et al.  Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. , 2004, Proteins.

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

[183]  D. Baker,et al.  Modeling structurally variable regions in homologous proteins with rosetta , 2004, Proteins.

[184]  R. A. George,et al.  Snapdragon: a Method to Delineate Protein Structural Domains from Sequence Data , 2022 .

[185]  H. Berendsen,et al.  A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.

[186]  Shoshana J. Wodak,et al.  Location of structural domains in proteins , 1981 .

[187]  Ilya N. Shindyalov,et al.  PDP: protein domain parser , 2003, Bioinform..

[188]  Z. Weng,et al.  ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.

[189]  Zheng Yuan,et al.  SVMtm: Support vector machines to predict transmembrane segments , 2004, J. Comput. Chem..

[190]  J. Skolnick,et al.  Automated structure prediction of weakly homologous proteins on a genomic scale. , 2004, Proceedings of the National Academy of Sciences of the United States of America.