FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions
暂无分享,去创建一个
[1] Dario Ghersi,et al. SITEHOUND-web: a server for ligand binding site identification in protein structures , 2009, Nucleic Acids Res..
[2] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[3] Ross Ihaka,et al. Lexical Scope and Statistical Computing , 2000 .
[4] Gonzalo López,et al. Assessment of ligand binding residue predictions in CASP8 , 2009, Proteins.
[5] Michael J E Sternberg,et al. Prediction of ligand binding sites using homologous structures and conservation at CASP8 , 2009, Proteins.
[6] Michael I. Jordan,et al. Active site prediction using evolutionary and structural information , 2010, Bioinform..
[7] Arne Elofsson,et al. Assessment of global and local model quality in CASP8 using Pcons and ProQ , 2009, Proteins.
[8] Nir Ben-Tal,et al. Quality assessment of protein model-structures using evolutionary conservation , 2010, Bioinform..
[9] Yang Zhang,et al. I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.
[10] C. D. Andersson,et al. Mapping of ligand‐binding cavities in proteins , 2010, Proteins.
[11] Jianlin Cheng,et al. Evaluating the absolute quality of a single protein model using structural features and support vector machines , 2009, Proteins.
[12] Silvio C. E. Tosatto,et al. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust , 2009, Proteins.
[13] Alfonso Valencia,et al. firestar—advances in the prediction of functionally important residues , 2011, Nucleic Acids Res..
[14] Liam J. McGuffin,et al. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments , 2010, Bioinform..
[15] Liam J. McGuffin,et al. FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins , 2011, BMC Bioinformatics.
[16] Kimmen Sjölander,et al. INTREPID: a web server for prediction of functionally important residues by evolutionary analysis , 2009, Nucleic Acids Res..
[17] Tal Pupko,et al. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids , 2010, Nucleic Acids Res..
[18] Michael J. E. Sternberg,et al. 3DLigandSite: predicting ligand-binding sites using similar structures , 2010, Nucleic Acids Res..
[19] Johannes Söding,et al. Prediction of protein functional residues from sequence by probability density estimation , 2008, Bioinform..
[20] Thomas Lengauer,et al. ROCR: visualizing classifier performance in R , 2005, Bioinform..
[21] Costas D Maranas,et al. Recent advances in computational protein design. , 2011, Current opinion in structural biology.
[22] Liam J. McGuffin,et al. The binding site distance test score: a robust method for the assessment of predicted protein binding sites , 2010, Bioinform..
[23] Kai Wang,et al. Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information , 2008, PLoS Comput. Biol..
[24] Keehyoung Joo,et al. Protein‐binding site prediction based on three‐dimensional protein modeling , 2009, Proteins.
[25] M. Schroeder,et al. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation , 2006, BMC Structural Biology.
[26] J. Hanley,et al. The meaning and use of the area under a receiver operating characteristic (ROC) curve. , 1982, Radiology.
[27] Janet M. Thornton,et al. WSsas: a web service for the annotation of functional residues through structural homologues , 2009, Bioinform..
[28] Pascal Benkert,et al. QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.
[29] Daniel B. Roche,et al. Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method , 2011, Proteins.
[30] Jacob de Vlieg,et al. ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs , 2011, BMC Bioinformatics.
[31] Jianlin Cheng,et al. Prediction of global and local quality of CASP8 models by MULTICOM series , 2009, Proteins.
[32] Chuan Yi Tang,et al. Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules , 2010, Bioinform..
[33] Torsten Schwede,et al. Assessment of ligand‐binding residue predictions in CASP9 , 2011, Proteins.
[34] Ricardo Núñez Miguel. Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families , 2004, Bioinform..
[35] Ajay N. Jain,et al. Surface‐based protein binding pocket similarity , 2011, Proteins.
[36] Alfonso Valencia,et al. firestar—prediction of functionally important residues using structural templates and alignment reliability , 2007, Nucleic Acids Res..
[37] Jianlin Cheng,et al. APOLLO: a quality assessment service for single and multiple protein models , 2011, Bioinform..
[38] Michael J. E. Sternberg,et al. ConFunc - functional annotation in the twilight zone , 2008, Bioinform..
[39] 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.
[40] Anna Tramontano,et al. The prediction of protein function at CASP6 , 2005, Proteins.
[41] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.