Structure based approach for understanding organism specific recognition of protein-RNA complexes
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Masakazu Sekijima | M Michael Gromiha | Sonia Pankaj Chothani | Chandrasekaran Ramakrishnan | Raju Nagarajan
[1] Gabriele Varani,et al. Protein families and RNA recognition , 2005, The FEBS journal.
[2] Holger Gohlke,et al. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.
[3] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[4] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[5] Avinash Bhandoola,et al. Biology Direct , 2006 .
[6] G. Eriani,et al. The structure of an AspRS—tRNAAsp complex reveals a tRNA‐dependent control mechanism , 2001, The EMBO journal.
[7] J. Janin,et al. Dissecting protein–RNA recognition sites , 2008, Nucleic acids research.
[8] D. Moras,et al. An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. , 2000, Journal of molecular biology.
[9] Harianto Tjong,et al. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces , 2007, Nucleic acids research.
[10] Masaki Yamamoto,et al. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein , 2010, Nature.
[11] Kristian Rother,et al. RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures , 2012, BMC Bioinformatics.
[12] P. Kollman,et al. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.
[13] Shandar Ahmad,et al. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information , 2004, Bioinform..
[14] M. Gromiha,et al. Energy based approach for understanding the recognition mechanism in protein-protein complexes. , 2009, Molecular bioSystems.
[15] B Jayaram,et al. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes , 2011, Proteome Science.
[16] P. Gardner,et al. Annotating RNA motifs in sequences and alignments , 2014, bioRxiv.
[17] T. Glisovic,et al. RNA‐binding proteins and post‐transcriptional gene regulation , 2008, FEBS letters.
[18] J. Bujnicki,et al. Computational methods for prediction of protein-RNA interactions. , 2012, Journal of structural biology.
[19] M. Michael Gromiha,et al. SRide: a server for identifying stabilizing residues in proteins , 2005, Nucleic Acids Res..
[20] Xiang-Sun Zhang,et al. De novo prediction of RNA-protein interactions from sequence information. , 2013, Molecular bioSystems.
[21] Vasant Honavar,et al. Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art , 2012, BMC Bioinformatics.
[22] M. Michael Gromiha,et al. Prediction of RNA Binding Residues: An Extensive Analysis Based on Structure and Function to Select the Best Predictor , 2014, PloS one.
[23] M Michael Gromiha,et al. Discrimination of mesophilic and thermophilic proteins using machine learning algorithms , 2007, Proteins.
[24] Oriol Fornes,et al. On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions. , 2014, Advances in protein chemistry and structural biology.
[25] 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..
[26] Jack Y. Yang,et al. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features , 2010, BMC Syst. Biol..
[27] Vasant Honavar,et al. PRIDB: a protein–RNA interface database , 2010, Nucleic Acids Res..
[28] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[29] Tal Pupko,et al. Structural Genomics , 2005 .
[30] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[31] D. Moras,et al. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp) , 1991, Science.
[32] Xiaojie Xu,et al. Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models , 2006 .
[33] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.
[34] Sandeep Kumar,et al. GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies , 2014, Bioinform..
[35] Gary J. Olsen,et al. Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.
[36] John SantaLucia,et al. AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA. , 2007, Journal of chemical theory and computation.
[37] M. Michael Gromiha,et al. Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach , 2010, ICIC.
[38] R. Nagarajan,et al. Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins , 2013, Nucleic acids research.
[39] S. Jones,et al. Protein-RNA interactions: a structural analysis. , 2001, Nucleic acids research.
[40] Ruth Nussinov,et al. RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases , 2009, Nucleic Acids Res..
[41] Daniel Herschlag,et al. Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System , 2008, PLoS biology.
[42] David S. Goodsell,et al. The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..
[43] Suncica Z. Borozan,et al. Cation-π interactions in high resolution protein-RNA complex crystal structures , 2013, Comput. Biol. Chem..
[44] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[45] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[46] Gajendra P.S. Raghava,et al. Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.
[47] M Michael Gromiha,et al. Understanding the recognition mechanism of protein-RNA complexes using energy based approach. , 2010, Current protein & peptide science.