Tasser‐Based Protein Structure Prediction

[1]  New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997 .

[2]  George Karypis,et al.  Profile-based direct kernels for remote homology detection and fold recognition , 2005, Bioinform..

[3]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

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

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

[6]  Michal Brylinski,et al.  Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints , 2008, J. Comput. Chem..

[7]  Michael R. Shirts,et al.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. , 2003, Biopolymers.

[8]  T L Blundell,et al.  An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. , 1993, Protein engineering.

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

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

[11]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[12]  Hongyi Zhou,et al.  Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition , 2004, Proteins.

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

[14]  J. Lahiri,et al.  G protein-coupled receptor microarrays for drug discovery. , 2003, Drug discovery today.

[15]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[16]  J. Skolnick,et al.  A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation , 2008, Proceedings of the National Academy of Sciences.

[17]  Hongyi Zhou,et al.  A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding , 2004, Proteins.

[18]  Roland L Dunbrack,et al.  Assessment of fold recognition predictions in CASP6 , 2005, Proteins.

[19]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[20]  Torsten Schwede,et al.  Assessment of CASP7 predictions for template‐based modeling targets , 2007, Proteins.

[21]  Y Shan,et al.  Fold recognition and accurate query‐template alignment by a combination of PSI‐BLAST and threading , 2001, Proteins.

[22]  K. Dill,et al.  Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.

[23]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[24]  A. Sali,et al.  Statistical potentials for fold assessment , 2009 .

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

[26]  J. Skolnick,et al.  Structure‐based classification of 45 FK506‐binding proteins , 2008, Proteins.

[27]  Manuel C. Peitsch,et al.  SWISS-MODEL: an automated protein homology-modeling server , 2003, Nucleic Acids Res..

[28]  A. Liwo,et al.  Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[29]  J. Skolnick,et al.  The PDB is a covering set of small protein structures. , 2003, Journal of molecular biology.

[30]  Edgar Jacoby,et al.  Chemogenomics knowledge-based strategies in drug discovery. , 2003, Drug news & perspectives.

[31]  J. Skolnick,et al.  A distance‐dependent atomic knowledge‐based potential for improved protein structure selection , 2001, Proteins.

[32]  J. Skolnick,et al.  Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm , 2004, Proteins.

[33]  Shashi B. Pandit,et al.  SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes , 2002, Nucleic Acids Res..

[34]  J. Skolnick,et al.  TOUCHSTONE II: a new approach to ab initio protein structure prediction. , 2003, Biophysical journal.

[35]  Yang Zhang,et al.  TASSER-Lite: an automated tool for protein comparative modeling. , 2006, Biophysical journal.

[36]  Seung Yup Lee,et al.  Development and benchmarking of TASSERiter for the iterative improvement of protein structure predictions , 2007, Proteins.

[37]  Yang Zhang,et al.  The protein structure prediction problem could be solved using the current PDB library. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Yang Zhang,et al.  TASSER: An automated method for the prediction of protein tertiary structures in CASP6 , 2005, Proteins.

[39]  Jeffrey Skolnick,et al.  Protein structure prediction by pro-Sp3-TASSER. , 2009, Biophysical journal.

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

[41]  Adam Liwo,et al.  Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes , 2001 .

[42]  J. Skolnick,et al.  Ab initio modeling of small proteins by iterative TASSER simulations , 2007, BMC Biology.

[43]  Yang Zhang,et al.  TASSER‐based refinement of NMR structures , 2006, Proteins.

[44]  Yang Zhang,et al.  SPICKER: A clustering approach to identify near‐native protein folds , 2004, J. Comput. Chem..

[45]  Charles L. Brooks,et al.  Identifying native‐like protein structures using physics‐based potentials , 2002, J. Comput. Chem..

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

[47]  J. Skolnick,et al.  Benchmarking of dimeric threading and structure refinement , 2006, Proteins.

[48]  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.

[49]  T. Lundstedt,et al.  Classification of G‐protein coupled receptors by alignment‐independent extraction of principal chemical properties of primary amino acid sequences , 2002, Protein science : a publication of the Protein Society.

[50]  J. Skolnick,et al.  Benchmarking of TASSER in the ab initio limit , 2007, Proteins: Structure, Function, and Bioinformatics.

[51]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[52]  W. Sadee,et al.  Evolutionary relationships among G protein-coupled receptors using a clustered database approach , 2001, AAPS PharmSci.

[53]  Seung Yup Lee,et al.  Analysis of TASSER‐based CASP7 protein structure prediction results , 2007, Proteins.

[54]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[55]  Manfred J. Sippl,et al.  Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures , 1993, J. Comput. Aided Mol. Des..

[56]  S. Mitaku,et al.  Identification of G protein‐coupled receptor genes from the human genome sequence , 2002, FEBS letters.

[57]  J. Skolnick,et al.  Ab initio protein structure prediction using chunk-TASSER. , 2007, Biophysical journal.

[58]  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.

[59]  J Skolnick,et al.  Defrosting the frozen approximation: PROSPECTOR— A new approach to threading , 2001, Proteins.

[60]  R. Stevens,et al.  The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist , 2008, Science.

[61]  Jacquelyn S. Fetrow,et al.  Structural genomics and its importance for gene function analysis , 2000, Nature Biotechnology.

[62]  J. Skolnick,et al.  EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. , 2004, Nucleic acids research.

[63]  J. Skolnick,et al.  On the origin and highly likely completeness of single-domain protein structures. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[64]  J. Skolnick.  In quest of an empirical potential for protein structure prediction. , 2006, Current opinion in structural biology.

[65]  P. Bradley,et al.  Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.

[66]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[67]  Jeffrey Skolnick,et al.  Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. , 2008, Biophysical journal.

[68]  M. Gerstein.  Patterns of protein‐fold usage in eight microbial genomes: A comprehensive structural census , 1998, Proteins.

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

[70]  R. Stevens,et al.  High-Resolution Crystal Structure of an Engineered Human β2-Adrenergic G Protein–Coupled Receptor , 2007, Science.

[71]  Alfonso Valencia,et al.  Assessment of predictions submitted for the CASP6 comparative modeling category , 2005, Proteins.

[72]  S F Altschul,et al.  Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. , 1998, Trends in biochemical sciences.

[73]  Jeffrey Skolnick,et al.  Fast procedure for reconstruction of full‐atom protein models from reduced representations , 2008, J. Comput. Chem..

[74]  S. Hubbard,et al.  Conservation of orientation and sequence in protein domain--domain interactions. , 2005, Journal of molecular biology.

[75]  Robert B. Russell,et al.  Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures , 2003, Nucleic Acids Res..

[76]  J. Skolnick,et al.  Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding , 2002, Proteins.

[77]  Yang Zhang,et al.  Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. , 2004, Biophysical journal.

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

[79]  Yang Zhang,et al.  Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome , 2006, PLoS Comput. Biol..

[80]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[81]  R. Fleischmann,et al.  The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.

[82]  Liliana Wroblewska,et al.  Protein model refinement using an optimized physics-based all-atom force field , 2008, Proceedings of the National Academy of Sciences.

[83]  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.

[84]  J. Skolnick,et al.  How well is enzyme function conserved as a function of pairwise sequence identity? , 2003, Journal of molecular biology.

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

[86]  Liam J. McGuffin,et al.  Improvement of the GenTHREADER Method for Genomic Fold Recognition , 2003, Bioinform..

[87]  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 .