VoroMQA: Assessment of protein structure quality using interatomic contact areas
暂无分享,去创建一个
[1] Alexandre G. de Brevern,et al. VLDP web server: a powerful geometric tool for analysing protein structures in their environment , 2013, Nucleic Acids Res..
[2] Adam Zemla,et al. LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..
[3] Yang Zhang,et al. Scoring function for automated assessment of protein structure template quality , 2004, Proteins.
[4] F. Wilcoxon. Individual Comparisons by Ranking Methods , 1945 .
[5] Nick V. Grishin,et al. Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models , 2016, PloS one.
[6] Johannes Söding,et al. Fast and accurate automatic structure prediction with HHpred , 2009, Proteins.
[7] B. Rost,et al. Critical assessment of methods of protein structure prediction—Round VIII , 2009, Proteins.
[8] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[9] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[10] Anna Tramontano,et al. Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11 , 2016, Proteins.
[11] Anna Tramontano,et al. Assessment of the assessment: Evaluation of the model quality estimates in CASP10 , 2014, Proteins.
[12] David Baker,et al. Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..
[13] A. Poupon. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. , 2004, Current opinion in structural biology.
[14] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[15] Björn Wallner,et al. Improved model quality assessment using ProQ2 , 2012, BMC Bioinformatics.
[16] C Venclovas,et al. Processing and analysis of CASP3 protein structure predictions , 1999, Proteins.
[17] 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.
[18] Björn Wallner,et al. ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling , 2014, Bioinform..
[19] Kliment Olechnovič,et al. CAD‐score: A new contact area difference‐based function for evaluation of protein structural models , 2013, Proteins.
[20] Kliment Olechnovic,et al. Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure , 2011, Bioinform..
[21] Jianpeng Ma,et al. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. , 2008, Journal of molecular biology.
[22] Jacek Blazewicz,et al. SphereGrinder - reference structure-based tool for quality assessment of protein structural models , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[23] Leonidas J. Guibas,et al. Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials , 2006, Comput. Aided Geom. Des..
[24] J. Skolnick,et al. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. , 2011, Biophysical journal.
[25] Marco Biasini,et al. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests , 2013, Bioinform..
[26] Ernst-Walter Knapp,et al. Optimized distance‐dependent atom‐pair‐based potential DOOP for protein structure prediction , 2015, Proteins.
[27] Kristian Rother,et al. Voronoia: analyzing packing in protein structures , 2008, Nucleic Acids Res..
[28] Jilong Li,et al. A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11 , 2015, BMC Bioinformatics.
[29] Adam Zemla,et al. Critical assessment of methods of protein structure prediction (CASP)‐round V , 2005, Proteins.
[30] Yang Zhang,et al. I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.
[31] Kliment Olechnovic,et al. Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls , 2014, J. Comput. Chem..
[32] Rahim Jafari,et al. Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results. , 2016, Journal of molecular graphics & modelling.
[33] Yang Zhang,et al. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field , 2012, Proteins.
[34] Mehdi Sadeghi,et al. Delaunay‐based nonlocal interactions are sufficient and accurate in protein fold recognition , 2014, Proteins.
[35] A. Tramontano,et al. Critical assessment of methods of protein structure prediction: Progress and new directions in round XI , 2016, Proteins.
[36] Roland L. Dunbrack,et al. proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .
[37] Zheng Wang,et al. Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11 , 2016, Scientific Reports.
[38] Yaoqi Zhou,et al. Specific interactions for ab initio folding of protein terminal regions with secondary structures , 2008, Proteins.
[39] 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.
[40] Yang Zhang,et al. A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction , 2010, PloS one.
[41] M. Sippl. Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.
[42] B. McConkey,et al. Discrimination of native protein structures using atom–atom contact scoring , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[43] Juergen Haas,et al. The Protein Model Portal—a comprehensive resource for protein structure and model information , 2013, Database J. Biol. Databases Curation.
[44] A. Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.
[45] Karolis Uziela,et al. ProQ2: estimation of model accuracy implemented in Rosetta , 2016, Bioinform..
[46] Roland L Dunbrack,et al. Assessment of template‐based modeling of protein structure in CASP11 , 2016, Proteins.
[47] Renzhi Cao,et al. Protein single-model quality assessment by feature-based probability density functions , 2016, Scientific Reports.
[48] F. Richards. The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.
[49] Anna Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP) — round x , 2014, Proteins.
[50] Pascal Benkert,et al. QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.