Basic protein structure prediction for the biologist: A review
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[1] Johannes Söding,et al. The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..
[2] 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.
[3] Ron Elber,et al. Enriching the sequence substitution matrix by structural information , 2003, Proteins.
[4] Krzysztof Fidelis,et al. CASP8 results in context of previous experiments , 2009, Proteins.
[5] A Sali,et al. Comparative protein modeling by satisfaction of spatial restraints. , 1996, Molecular medicine today.
[6] András Fiser,et al. ModLoop: automated modeling of loops in protein structures , 2003, Bioinform..
[7] Cyrus Chothia,et al. The SUPERFAMILY database in 2007: families and functions , 2006, Nucleic Acids Res..
[8] A Sali,et al. Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity. , 1996, Journal of immunology.
[9] Ronald M Levy,et al. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. , 2003, Protein engineering.
[10] David L. Wheeler,et al. GenBank , 2015, Nucleic Acids Res..
[11] C. Sander,et al. Errors in protein structures , 1996, Nature.
[12] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[13] J. Skolnick,et al. The PDB is a covering set of small protein structures. , 2003, Journal of molecular biology.
[14] Lars Malmström,et al. Automated prediction of CASP‐5 structures using the Robetta server , 2003, Proteins.
[15] François Stricher,et al. The FoldX web server: an online force field , 2005, Nucleic Acids Res..
[16] Torsten Schwede,et al. Automated protein structure homology modeling: a progress report. , 2004, Pharmacogenomics.
[17] Cyrus Chothia,et al. SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny , 2008, Nucleic Acids Res..
[18] Yang Zhang,et al. I‐TASSER: Fully automated protein structure prediction in CASP8 , 2009, Proteins.
[19] Prasanna R Kolatkar,et al. Assessment of CASP7 structure predictions for template free targets , 2007, Proteins.
[20] A. Fiser. Protein structure modeling in the proteomics era , 2004, Expert review of proteomics.
[21] Arne Elofsson,et al. 3D-Jury: A Simple Approach to Improve Protein Structure Predictions , 2003, Bioinform..
[22] R. Elber,et al. Distance‐dependent, pair potential for protein folding: Results from linear optimization , 2000, Proteins.
[23] J Meller,et al. Linear programming optimization and a double statistical filter for protein threading protocols , 2001, Proteins.
[24] Alfonso Valencia,et al. Assessment of predictions submitted for the CASP7 function prediction category. , 2007, Proteins.
[25] M J Sternberg,et al. Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.
[26] 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 .
[27] T. Schwede,et al. Protein structure homology modeling using SWISS-MODEL workspace , 2008, Nature Protocols.
[28] M. Doherty,et al. A Random Mutagenesis Approach to Isolate Dominant-Negative Yeast sec1 Mutants Reveals a Functional Role for Domain 3a in Yeast and Mammalian Sec1/Munc18 Proteins , 2008, Genetics.
[29] Daisuke Kihara,et al. Quality assessment of protein structure models. , 2009, Current protein & peptide science.
[30] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[31] Yang Zhang. Progress and challenges in protein structure prediction. , 2008, Current opinion in structural biology.
[32] Torsten Schwede,et al. The SWISS-MODEL Repository and associated resources , 2008, Nucleic Acids Res..
[33] A. Fiser,et al. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[34] Richard Bonneau,et al. Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.
[35] David Kim,et al. Assessment of predictions submitted for the CASP7 domain prediction category , 2007, Proteins.
[36] Richard Bonneau,et al. De novo prediction of three-dimensional structures for major protein families. , 2002, Journal of molecular biology.
[37] A. Sali,et al. Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.
[38] Daniel Fischer,et al. Servers for protein structure prediction. , 2006, Current opinion in structural biology.
[39] Christophe Combet,et al. Geno3D: automatic comparative molecular modelling of protein , 2002, Bioinform..
[40] Marc A. Martí-Renom,et al. EVA: evaluation of protein structure prediction servers , 2003, Nucleic Acids Res..
[41] W U Primrose,et al. A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. , 1996, Biochemistry.
[42] Sitao Wu,et al. MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information , 2008, Proteins.
[43] Pascal Benkert,et al. QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.
[44] Cyrus Chothia,et al. The SUPERFAMILY database in 2004: additions and improvements , 2004, Nucleic Acids Res..
[45] Christophe G. Lambert,et al. ESyPred3D: Prediction of proteins 3D structures , 2002, Bioinform..
[46] M. Sternberg,et al. Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.
[47] G A Petsko,et al. Structure determination of turkey egg-white lysozyme using Laue diffraction data. , 1992, Acta crystallographica. Section B, Structural science.
[48] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[49] Lei Xie,et al. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling , 2003, Proteins.
[50] Narayanan Eswar,et al. MODBASE, a database of annotated comparative protein structure models , 2002, Nucleic Acids Res..
[51] Haruki Nakamura,et al. Data Deposition and Annotation at the Worldwide Protein Data Bank , 2009, Molecular biotechnology.
[52] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[53] M. Sternberg,et al. Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.
[54] Burkhard Rost,et al. META-PP: single interface to crucial prediction servers , 2003, Nucleic Acids Res..
[55] Yang Zhang,et al. I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.
[56] András Fiser,et al. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. , 2002, Biochemical and biophysical research communications.
[57] A. Sali,et al. Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.
[58] A. Kolinski. Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.
[59] Randy J Read,et al. Assessment of CASP7 predictions in the high accuracy template‐based modeling category , 2007, Proteins.
[60] B. Rost. PHD: predicting one-dimensional protein structure by profile-based neural networks. , 1996, Methods in enzymology.
[61] Yang Zhang. Protein structure prediction: when is it useful? , 2009, Current opinion in structural biology.
[62] Yang Zhang,et al. Template‐based modeling and free modeling by I‐TASSER in CASP7 , 2007, Proteins.
[63] Janusz M. Bujnicki,et al. GeneSilico protein structure prediction meta-server , 2003, Nucleic Acids Res..
[64] C. Lambert,et al. ESyPred 3 D : Prediction of proteins 3 D structures , 2002 .
[65] R Sánchez,et al. Evaluation of comparative protein structure modeling by MODELLER‐3 , 1997, Proteins.
[66] David Baker,et al. Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..
[67] Arne Elofsson,et al. All are not equal: A benchmark of different homology modeling programs , 2005, Protein science : a publication of the Protein Society.
[68] Z. Xiang,et al. Advances in homology protein structure modeling. , 2006, Current protein & peptide science.
[69] Sitao Wu,et al. LOMETS: A local meta-threading-server for protein structure prediction , 2007, Nucleic acids research.
[70] John Moult,et al. A unifold, mesofold, and superfold model of protein fold use , 2002, Proteins.
[71] M. Karplus,et al. Evaluation of comparative protein modeling by MODELLER , 1995, Proteins.
[72] Eaton E. Lattman,et al. Protein structure prediction: A special issue , 1995 .
[73] C. Chothia,et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.
[74] Adam Liwo,et al. Recent improvements in prediction of protein structure by global optimization of a potential energy function , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[75] Christodoulos A. Floudas,et al. Advances in protein structure prediction and de novo protein design : A review , 2006 .
[76] Yang Zhang,et al. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment , 2004, Bioinform..
[77] Torsten Schwede,et al. Assessment of CASP7 predictions for template‐based modeling targets , 2007, Proteins.
[78] A. Lesk,et al. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.
[79] C A Floudas,et al. Computational methods in protein structure prediction. , 2007, Biotechnology and bioengineering.
[80] Chris Sander,et al. Completeness in structural genomics , 2001, Nature Structural Biology.
[81] Ying Xu,et al. A historical perspective of template-based protein structure prediction. , 2008, Methods in molecular biology.
[82] D. Eisenberg,et al. VERIFY3D: assessment of protein models with three-dimensional profiles. , 1997, Methods in enzymology.
[83] 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.
[84] Samuel L. DeLuca,et al. Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You , 2010, Biochemistry.
[85] Daniel Fischer,et al. ‘Meta’Approaches to Protein Structure Prediction , 2008 .
[86] G Vriend,et al. WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.
[87] 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.
[88] I. Vakser. Protein docking for low-resolution structures. , 1995, Protein engineering.
[89] Alnawaz Rehemtulla,et al. CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature , 2007, Proceedings of the National Academy of Sciences.
[90] Manuel C. Peitsch,et al. Protein Modeling by E-mail , 1995, Bio/Technology.
[91] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[92] G Kolata. Trying to crack the second half of the genetic code. , 1986, Science.
[93] D. Baker,et al. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection , 2006, Nucleic acids research.
[94] Michael Nilges,et al. BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btl655 Structural bioinformatics Biskit—A software platform for structural bioinformatics , 2006 .