Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins
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R. Nagarajan | Shandar Ahmad | M. Michael Gromiha | R. Nagarajan | Shandar Ahmad | M. Michael Gromiha
[1] Yaoqi Zhou,et al. An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles , 2009, Proteins.
[2] H. Margalit,et al. A role for CH...O interactions in protein-DNA recognition. , 1998, Journal of molecular biology.
[3] Harianto Tjong,et al. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces , 2007, Nucleic acids research.
[4] R. Lavery,et al. Protein-DNA recognition triggered by a DNA conformational switch. , 2011, Angewandte Chemie.
[5] M. Michael Gromiha,et al. Scoring Function Based Approach for Locating Binding Sites and Understanding Recognition Mechanism of Protein-DNA Complexes , 2011, J. Chem. Inf. Model..
[6] The UniProt Consortium,et al. Reorganizing the protein space at the Universal Protein Resource (UniProt) , 2011, Nucleic Acids Res..
[7] Ozlem Keskin,et al. Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins , 2008, Nucleic acids research.
[8] Shandar Ahmad,et al. PSSM-based prediction of DNA binding sites in proteins , 2005, BMC Bioinformatics.
[9] Burkhard Rost,et al. Prediction of DNA-binding residues from sequence , 2007, ISMB/ECCB.
[10] Shandar Ahmad,et al. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information , 2004, Bioinform..
[11] Michael Schroeder,et al. MetaDBSite: a meta approach to improve protein DNA-binding sites prediction , 2011, BMC Systems Biology.
[12] R. H. Austin,et al. Importance of DNA stiffness in protein–DNA binding specificity , 1987, Nature.
[13] Ponraj Prabakaran,et al. Classification of protein-DNA complexes based on structural descriptors. , 2006, Structure.
[14] M M Gromiha,et al. Protein secondary structure prediction in different structural classes. , 1998, Protein engineering.
[15] H. Kono,et al. Structure‐based prediction of DNA target sites by regulatory proteins , 1999, Proteins.
[16] Akinori Sarai,et al. Thermodynamic database for protein-nucleic acid interactions (ProNIT) , 2001, Bioinform..
[17] H. Margalit,et al. Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. , 1998, Nucleic acids research.
[18] R. Mann,et al. The role of DNA shape in protein-DNA recognition , 2009, Nature.
[19] Jason E. Donald,et al. Energetics of protein–DNA interactions , 2006, Nucleic acids research.
[20] Samuel Selvaraj,et al. Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. , 2004, Journal of molecular biology.
[21] M. Gromiha,et al. Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. , 2013, Advances in protein chemistry and structural biology.
[22] Xiao Sun,et al. Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature , 2008, Bioinform..
[23] Marianne Rooman,et al. Cation-pi/H-bond stair motifs at protein-DNA interfaces. , 2002, Journal of molecular biology.
[24] Hui Lu,et al. NAPS: a residue-level nucleic acid-binding prediction server , 2010, Nucleic Acids Res..
[25] Peng Zhou,et al. Systematic Classification and Analysis of Themes in Protein-DNA Recognition , 2010, J. Chem. Inf. Model..
[26] Francisco Melo,et al. The Protein-DNA Interface database , 2010, BMC Bioinformatics.
[27] Liangjiang Wang,et al. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences , 2006, Nucleic Acids Res..
[28] Isabella Daidone,et al. Mechanism of DNA recognition by the restriction enzyme EcoRV. , 2010, Journal of molecular biology.
[29] S. Pongor,et al. The role of DNA bending in Cro protein-DNA interactions. , 1997, Biophysical chemistry.
[30] N. Bhardwaj,et al. Residue‐level prediction of DNA‐binding sites and its application on DNA‐binding protein predictions , 2007, FEBS letters.
[31] Anatoly B Kolomeisky,et al. Physics of protein-DNA interactions: mechanisms of facilitated target search. , 2011, Physical chemistry chemical physics : PCCP.
[32] V. Zhurkin,et al. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[33] Igor B. Kuznetsov,et al. DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins , 2007, Bioinform..
[34] Kentaro Shimizu,et al. A new method for evaluating the specificity of indirect readout in protein–DNA recognition , 2012, Nucleic acids research.
[35] M. Michael Gromiha,et al. Thermodynamic Database for Protein-Nucleic Acid Interactions , 1999 .
[36] A. R. Srinivasan,et al. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.
[37] M. Michael Gromiha,et al. Protein Bioinformatics: From Sequence to Function , 2010 .
[38] Liangjiang Wang,et al. Prediction of DNA-binding residues from protein sequence information using random forests , 2009, BMC Genomics.
[39] H. Kono,et al. Protein-DNA recognition patterns and predictions. , 2005, Annual review of biophysics and biomolecular structure.
[40] P E Bourne,et al. PRONUC: a software package for the analysis of protein and nucleic acid sequences. , 1987, Computer methods and programs in biomedicine.
[41] Leo Breiman,et al. Random Forests , 2001, Machine Learning.
[42] M Michael Gromiha,et al. Influence of DNA stiffness in protein-DNA recognition. , 2005, Journal of biotechnology.
[43] Sándor Pongor,et al. A simple probabilistic scoring method for protein domain identification , 2000, Bioinform..
[44] A. Das,et al. Free‐energy component analysis of 40 protein–DNA complexes: A consensus view on the thermodynamics of binding at the molecular level , 2002, J. Comput. Chem..
[45] Andrey G. Cherstvy. Electrostatic interactions in biological DNA-related systems. , 2011, Physical chemistry chemical physics : PCCP.
[46] G. Hong,et al. Nucleic Acids Research , 2015, Nucleic Acids Research.
[47] J. Silberg,et al. A transposase strategy for creating libraries of circularly permuted proteins , 2012, Nucleic acids research.
[48] Vasant Honavar,et al. Predicting DNA-binding sites of proteins from amino acid sequence , 2006, BMC Bioinformatics.
[49] Monika Fuxreiter,et al. Dynamic Protein–dna Recognition: beyond What Can Be Seen , 2022 .
[50] C. Pabo,et al. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? , 2000, Journal of molecular biology.
[51] Shinn-Ying Ho,et al. Design of accurate predictors for DNA-binding sites in proteins using hybrid SVM-PSSM method , 2007, Biosyst..
[52] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[53] Haruki Nakamura,et al. The Protein Data Bank at 40: reflecting on the past to prepare for the future. , 2012, Structure.
[54] M. Oda,et al. Thermodynamic and kinetic analyses for understanding sequence‐specific DNA recognition , 2000, Genes to cells : devoted to molecular & cellular mechanisms.
[55] Janet M Thornton,et al. Identifying DNA-binding proteins using structural motifs and the electrostatic potential. , 2004, Nucleic acids research.
[56] D. Lejeune,et al. Protein–nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure , 2005, Proteins.
[57] Jack Y. Yang,et al. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features , 2010, BMC Syst. Biol..
[58] K. Schulten,et al. Recognition of methylated DNA through methyl-CpG binding domain proteins , 2011, Nucleic acids research.
[59] M. Michael Gromiha,et al. Influence of cation–π interactions in protein–DNA complexes , 2004 .
[60] L. Mirny,et al. Structural analysis of conserved base pairs in protein-DNA complexes. , 2002, Nucleic acids research.
[61] Seungwoo Hwang,et al. Using evolutionary and structural information to predict DNA‐binding sites on DNA‐binding proteins , 2006, Proteins.
[62] M. Rooman,et al. Contribution of cation-pi interactions to the stability of protein-DNA complexes. , 2000, Journal of molecular biology.
[63] K Nadassy,et al. Structural features of protein-nucleic acid recognition sites. , 1999, Biochemistry.
[64] H M Berman,et al. Protein-DNA interactions: A structural analysis. , 1999, Journal of molecular biology.