Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level

By Nicholas M. Luscombe, Roman A. Laskowski, Janet M. Thornton. Nucleic Acids Res., 2001

951 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/984b704f72d91b4dbcba0bd0561dee3237acdf66

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Citations in the corpus

PISCES: recent improvements to a PDB sequence culling server (2005, background): “DNA-binding) ( 4 ). The criteria for limiting the list of sequences can be applied to each chain in a PDB file, to each entry as a whole or to the relationships between protein chains and entries.”
The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology (2002, background): “Long-range electrostatic forces are good candidates for orienting chain random motions towards correctly folded structure.”
Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease (2007, background): “These analyses have identified protein folds for DNA binding, together with a few general rules for the protein-mediated recognition of specific DNA bases (1,4,5).”
Identifying bacterial genes and endosymbiont DNA with Glimmer (2007, methodology): “This strategy of using a Gibbs-sampler to find RBS motifs in an iterative fashion was introduced in the GeneMarkS gene-finding system (Besemer et al., 2001).”
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. (2002, background): “– 12 Although the X-ray and NMR structures of over 200 DNA-binding proteins have been determined, few are of adequate quality to pinpoint solvent interactions accurately.(13) Those which are, have on average 12 water molecules located in positions mediating protein–DNA interactions.”
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles (2015, background): “Even though such models perform well overall (22), it has been recurrently shown that some TFs significantly benefit from more complex models when predicting TFBSs (2,23,24).”
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (2008, background): “Most regulatory proteins and many enzymes, by contrast, recognize specific, sequence-dependent structural features of individual base pairs, making direct contact with DNA atoms unique to their binding site”
Protein Arginine Methylation in Mammals: Who, What, and Why (2009, background): “In protein-DNA complexes, arginine residues are the most frequent hydrogen bond donors to backbone phosphate groups and to thymine, adenine, and guanine bases (Luscombe et al., 2001).”
How RNA binding proteins interact with RNA: molecules and mechanisms (2020, background): “Differences from Protein-DNA Interactions Similar analyses of protein-DNA structures allow comparison with protein-RNA interactions (Jones et al., 2001; Luscombe et al., 2001; Wilson et al., 2016).”
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences (2006, background): “At the atomic level, the interactions involve a complex combination of hydrogen bonds, van der Waals contacts and water-mediated bonds between amino acid residues and nucleotide bases (4,5).”