Homology modeling: Developing 3D structures of target proteins missing in databases

[1]  Alejandra Leo-Macias,et al.  An efficient conformational sampling method for homology modeling , 2008, Proteins.

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

[3]  F E Cohen,et al.  Novel method for the rapid evaluation of packing in protein structures. , 1990, Journal of molecular biology.

[4]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[5]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[6]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[7]  Om Silakari,et al.  Decoding the signature of molecular mechanism involved in mutation associated resistance to 1, 3-benzothiazin-4-ones (Btzs) based DprE1 inhibitors using BTZ043 as a reference drug , 2019, Molecular Simulation.

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

[9]  J. Pellequer,et al.  Does conformational free energy distinguish loop conformations in proteins? , 1997, Biophysical journal.

[10]  J. Garnier,et al.  Modeling of protein loops by simulated annealing , 1993, Protein science : a publication of the Protein Society.

[11]  Jianlin Cheng.  A multi-template combination algorithm for protein comparative modeling , 2008, BMC Structural Biology.

[12]  Zukang Feng,et al.  The Protein Data Bank and structural genomics , 2003, Nucleic Acids Res..

[13]  A. Kidera,et al.  Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation. , 1998, Journal of molecular biology.

[14]  Erik L. L. Sonnhammer,et al.  Automatic assessment of alignment quality , 2005, Nucleic acids research.

[15]  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.

[16]  Peer Bork,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[17]  Chuong B. Do,et al.  ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.

[18]  S. Pietrokovski.  Searching databases of conserved sequence regions by aligning protein multiple-alignments. , 1996, Nucleic acids research.

[19]  J. M. Sauder,et al.  Large‐scale comparison of protein sequence alignment algorithms with structure alignments , 2000, Proteins.

[20]  Christopher J. R. Illingworth,et al.  Identifying subset errors in multiple sequence alignments , 2014, Journal of biomolecular structure & dynamics.

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

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

[23]  C Sander,et al.  Polarity as a criterion in protein design. , 1989, Protein engineering.

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

[25]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[26]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[27]  C. Sander,et al.  Evaluation of protein models by atomic solvation preference. , 1992, Journal of molecular biology.

[28]  Stefano Moro,et al.  Linear and Nonlinear 3D-QSAR Approaches in Tandem with Ligand-Based Homology Modeling as a Computational Strategy To Depict the Pyrazolo-Triazolo-Pyrimidine Antagonists Binding Site of the Human Adenosine A2A Receptor , 2008, J. Chem. Inf. Model..

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

[30]  Arne Elofsson,et al.  Using multiple templates to improve quality of homology models in automated homology modeling , 2008, Protein science : a publication of the Protein Society.

[31]  Lars Malmström,et al.  Automated prediction of CASP‐5 structures using the Robetta server , 2003, Proteins.

[32]  William R Pearson,et al.  BLAST and FASTA similarity searching for multiple sequence alignment. , 2014, Methods in molecular biology.

[33]  Torsten Schwede,et al.  BIOINFORMATICS Bioinformatics Advance Access published November 12, 2005 The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling , 2022 .

[34]  Olivier Poch,et al.  RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments , 2003, Bioinform..

[35]  C. Sander,et al.  Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. , 1991, Journal of molecular biology.

[36]  Narayanan Eswar,et al.  Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.

[37]  M. Levitt.  Accurate modeling of protein conformation by automatic segment matching. , 1992, Journal of molecular biology.

[38]  Barry Honig,et al.  GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. , 2003, Methods in enzymology.

[39]  D. Haussler,et al.  Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.

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

[41]  Robert C. Edgar,et al.  Multiple sequence alignment. , 2006, Current opinion in structural biology.

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

[43]  G. Montelione,et al.  Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. , 2008, Structure.

[44]  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.

[45]  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 .

[46]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[47]  S. Wodak,et al.  Modelling the polypeptide backbone with 'spare parts' from known protein structures. , 1989, Protein engineering.

[48]  K. Ginalski.  Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.

[49]  R. Doolittle,et al.  Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.

[50]  T L Blundell,et al.  A database of globular protein structural domains: clustering of representative family members into similar folds. , 1996, Folding & design.

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

[52]  Olivier Poch,et al.  A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..

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

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

[55]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

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

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

[58]  Celia W G van Gelder,et al.  A molecular dynamics approach for the generation of complete protein structures from limited coordinate data , 1994, Proteins.

[59]  Chaok Seok,et al.  Protein loop modeling by using fragment assembly and analytical loop closure , 2010, Proteins.

[60]  Ram Samudrala,et al.  Improving the accuracy of template-based predictions by mixing and matching between initial models , 2008, BMC Structural Biology.

[61]  Nick V. Grishin,et al.  Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs , 2004, Bioinform..

[62]  B. Honig,et al.  Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials , 2008, Proteins.

[63]  O. Silakari,et al.  hCES1 and hCES2 mediated activation of epalrestat-antioxidant mutual prodrugs: Unwinding the hydrolytic mechanism using in silico approaches. , 2019, Journal of molecular graphics & modelling.

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

[65]  Sebastian Maurer-Stroh,et al.  Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins , 2011, Biology Direct.

[66]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[67]  R. Hilgenfeld,et al.  Utility of homology models in the drug discovery process , 2004, Drug Discovery Today.

[68]  A. Goede,et al.  Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. , 2003, Protein engineering.

[69]  Jakub Pas,et al.  Application of 3D‐Jury, GRDB, and Verify3D in fold recognition , 2003, Proteins.

[70]  Leszek Rychlewski,et al.  FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..

[71]  B. Honig,et al.  Free energy determinants of tertiary structure and the evaluation of protein models , 2000, Protein science : a publication of the Protein Society.

[72]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[73]  M Levitt,et al.  Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins , 1998, Protein science : a publication of the Protein Society.

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

[75]  A. Fiser.  Template-based protein structure modeling. , 2010, Methods in molecular biology.

[76]  Z. Xiang,et al.  Advances in homology protein structure modeling. , 2006, Current protein & peptide science.

[77]  Torsten Schwede,et al.  The SWISS-MODEL Repository and associated resources , 2008, Nucleic Acids Res..

[78]  Osvaldo Olmea,et al.  MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison , 2002, Protein science : a publication of the Protein Society.