Computational tools for protein–DNA interactions
C Kauffman, G Karypis - Wiley Interdisciplinary Reviews: Data …, 2012 - Wiley Online Library
Interactions between deoxyribonucleic acid (DNA) and proteins are central to living systems,
and characterizing how and when they occur would greatly enhance our understanding of …
and characterizing how and when they occur would greatly enhance our understanding of …
Understanding the mechanisms of protein-DNA interactions
R Lavery - APS March Meeting Abstracts, 2004 - ui.adsabs.harvard.edu
Structural, biochemical and thermodynamic data on protein-DNA interactions show that
specific recognition cannot be reduced to a simple set of binary interactions between the …
specific recognition cannot be reduced to a simple set of binary interactions between the …
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties
Interactions between proteins and nucleic acids are at the heart of many essential biological
processes. Despite increasing structural information about how these interactions may take …
processes. Despite increasing structural information about how these interactions may take …
Challenges and current status of computational methods for docking small molecules to nucleic acids
Since the development of the first docking program in 1982, the use of docking-based in
silico screening for potentially bioactive molecule discovery has become a common strategy …
silico screening for potentially bioactive molecule discovery has become a common strategy …
Interactions of Proteins with Nucleic Acids: from Structure to Specificity
D Jakubec - 2020 - dspace.cuni.cz
Sequence-specific interactions between proteins and nucleic acids play an essential role in
the cell biology. While several molecular mechanisms contributing to the binding speci-ficity …
the cell biology. While several molecular mechanisms contributing to the binding speci-ficity …
Dynamic and structural modeling of the specificity in protein–DNA interactions guided by binding assay and structure data
How transcription factors (TFs) recognize their DNA sequences is often investigated
complementarily by high-throughput protein binding assays and by structural biology …
complementarily by high-throughput protein binding assays and by structural biology …
Molecular docking
Molecular docking (MD) is one of the commonly used method to predict the orientation of
two molecules bound in a stable complex. Elucidation of knowledge about the preferred …
two molecules bound in a stable complex. Elucidation of knowledge about the preferred …
Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations
A van der Vaart - Biochimica et Biophysica Acta (BBA)-General Subjects, 2015 - Elsevier
Background Protein-DNA binding often involves dramatic conformational changes such as
protein folding and DNA bending. While thermodynamic aspects of this behavior are …
protein folding and DNA bending. While thermodynamic aspects of this behavior are …
Computational approaches for understanding the recognition mechanism of protein complexes
MM GROMIHA - Biomolecular Forms and Functions: A Celebration …, 2013 - World Scientific
Understanding the recognition mechanism of proteins with other molecules is a challenging
task in molecular and computational biology. Experiments provide a wealth of data on …
task in molecular and computational biology. Experiments provide a wealth of data on …
DNA simulation benchmarks as revealed by X-ray structures
WK Olson, AV Colasanti, Y Li, W Ge, G Zheng… - … Studies of RNA and …, 2006 - Springer
The inferences that can be drawn from known DNA structures provide new stimuli for
improvement of nucleic acid force fields and fresh ideas for exploration of the sequence …
improvement of nucleic acid force fields and fresh ideas for exploration of the sequence …