Toward the estimation of the absolute quality of individual protein structure models
暂无分享,去创建一个
Marco Biasini | Pascal Benkert | Torsten Schwede | T. Schwede | P. Benkert | M. Biasini | Pascal Benkert
[1] B. Matthews,et al. Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution. , 1987, Journal of molecular biology.
[2] Liam J. McGuffin,et al. Improving sequence-based fold recognition by using 3D model quality assessment , 2005, Bioinform..
[3] Pierre Baldi,et al. SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs , 2008, BMC Structural Biology.
[4] Roberto Dominguez,et al. Toxofilin from Toxoplasma gondii forms a ternary complex with an antiparallel actin dimer , 2007, Proceedings of the National Academy of Sciences.
[5] S. White,et al. Biophysical dissection of membrane proteins , 2009, Nature.
[6] L. Poppe,et al. Hepcidin Revisited, Disulfide Connectivity, Dynamics, and Structure , 2009, The Journal of Biological Chemistry.
[7] A. Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.
[8] T. Schwede,et al. Protein structure homology modeling using SWISS-MODEL workspace , 2008, Nature Protocols.
[9] Arne Svejgaard,et al. Crystal structure of HLA-DQ0602 that protects against type 1 diabetes and confers strong susceptibility to narcolepsy , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[10] S Clum,et al. Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. , 1999, The Journal of biological chemistry.
[11] Marco Biasini,et al. OpenStructure: a flexible software framework for computational structural biology , 2010, Bioinform..
[12] A. Elofsson,et al. Can correct protein models be identified? , 2003, Protein science : a publication of the Protein Society.
[13] R. Padmanabhan,et al. Dengue Virus NS3 Serine Protease , 1999, The Journal of Biological Chemistry.
[14] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[15] Torsten Schwede,et al. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling , 2006, Bioinform..
[16] Pierre Baldi,et al. SCRATCH: a protein structure and structural feature prediction server , 2005, Nucleic Acids Res..
[17] Adam Godzik,et al. Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. , 2005, Structure.
[18] Takeshi Wada,et al. Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding* , 2008, Journal of Biological Chemistry.
[19] Robert W. Janes,et al. The crystal structure of human endothelin , 1994, Nature Structural Biology.
[20] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[21] Liam J. McGuffin,et al. The ModFOLD server for the quality assessment of protein structural models , 2008, Bioinform..
[22] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[23] Manfred J. Sippl,et al. Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..
[24] F. Melo,et al. Assessing protein structures with a non-local atomic interaction energy. , 1998, Journal of molecular biology.
[25] Manuel C. Peitsch,et al. SWISS-MODEL: an automated protein homology-modeling server , 2003, Nucleic Acids Res..
[26] A. Sali,et al. How well can the accuracy of comparative protein structure models be predicted? , 2008, Protein science : a publication of the Protein Society.
[27] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[28] Adam Zemla,et al. LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..
[29] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[30] Anna Tramontano,et al. Evaluation of CASP8 model quality predictions , 2009, Proteins.
[31] Bernard Joris,et al. Standardized evaluation of protein stability. , 2010, Biochimica et biophysica acta.
[32] Anna Tramontano,et al. Critical assessment of methods of protein structure prediction—Round VII , 2007, Proteins.
[33] S. Bryant,et al. Critical assessment of methods of protein structure prediction (CASP): Round II , 1997, Proteins.
[34] T. Schwede,et al. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information , 2009, BMC Structural Biology.
[35] Silvio C. E. Tosatto,et al. The Victor/FRST Function for Model Quality Estimation , 2005, J. Comput. Biol..
[36] András Fiser,et al. New statistical potential for quality assessment of protein models and a survey of energy functions , 2010, BMC Bioinformatics.
[37] C. Eigenbrot,et al. X-ray structure of human relaxin at 1.5 A. Comparison to insulin and implications for receptor binding determinants. , 1991, Journal of molecular biology.
[38] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[39] Marc A. Martí-Renom,et al. EVA: evaluation of protein structure prediction servers , 2003, Nucleic Acids Res..
[40] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[41] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[42] References , 1971 .
[43] Pascal Benkert,et al. QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.
[44] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[45] K. Henrick,et al. Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.
[46] Adam Godzik,et al. Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.
[47] Roland L Dunbrack,et al. Outcome of a workshop on applications of protein models in biomedical research. , 2009, Structure.
[48] R. Padmanabhan,et al. Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. , 2009, The Journal of Biological Chemistry.
[49] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[50] Jianlin Cheng,et al. Evaluating the absolute quality of a single protein model using structural features and support vector machines , 2009, Proteins.
[51] Adam Godzik,et al. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. , 2006, Journal of molecular biology.
[52] Anna Tramontano,et al. Exploiting evolutionary relationships for predicting protein structures , 2003, Biotechnology and bioengineering.
[53] Roland L. Dunbrack. Sequence comparison and protein structure prediction. , 2006, Current opinion in structural biology.
[54] Pascal Benkert,et al. QMEAN server for protein model quality estimation , 2009, Nucleic Acids Res..
[55] Randy J Read,et al. Automated server predictions in CASP7 , 2007, Proteins.
[56] A. Kossiakoff,et al. X-ray structure of human relaxin at 1·5Å , 1991 .
[57] SödingJohannes. Protein homology detection by HMM--HMM comparison , 2005 .
[58] M. Sippl. Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.
[59] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.