Comprehensive review and empirical analysis of hallmarks of DNA-, RNA-and protein-binding residues in protein chains
Proteins interact with a variety of molecules including proteins and nucleic acids. We review
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …
Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naive Bayes
W Lou, X Wang, F Chen, Y Chen, B Jiang, H Zhang - PloS one, 2014 - journals.plos.org
Developing an efficient method for determination of the DNA-binding proteins, due to their
vital roles in gene regulation, is becoming highly desired since it would be invaluable to …
vital roles in gene regulation, is becoming highly desired since it would be invaluable to …
A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond
Proteins interact with diverse ligands to perform a large number of biological functions, such
as gene expression and signal transduction. Accurate identification of these protein–ligand …
as gene expression and signal transduction. Accurate identification of these protein–ligand …
CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks
DNA-binding proteins play a vital role in biological activity including DNA replication, DNA
packing, and DNA reparation. DNA-binding proteins can be classified into single-stranded …
packing, and DNA reparation. DNA-binding proteins can be classified into single-stranded …
A large-scale assessment of nucleic acids binding site prediction programs
Computational prediction of nucleic acid binding sites in proteins are necessary to
disentangle functional mechanisms in most biological processes and to explore the binding …
disentangle functional mechanisms in most biological processes and to explore the binding …
Improved DNA-binding protein identification by incorporating evolutionary information into the Chou's PseAAC
DNA-binding proteins play critical roles in various cellular biological processes, such as
gene expression and transcription. However, the experimental methods to identify these …
gene expression and transcription. However, the experimental methods to identify these …
DNABind: A hybrid algorithm for structure‐based prediction of DNA‐binding residues by combining machine learning‐and template‐based approaches
R Liu, J Hu - PROTEINS: structure, Function, and Bioinformatics, 2013 - Wiley Online Library
Accurate prediction of DNA‐binding residues has become a problem of increasing
importance in structural bioinformatics. Here, we presented DNABind, a novel hybrid …
importance in structural bioinformatics. Here, we presented DNABind, a novel hybrid …
DeepDBS: identification of DNA-binding sites in protein sequences by using deep representations and random forest
Interactions of biological molecules in organisms are considered to be primary factors for the
lifecycle of that organism. Various important biological functions are dependent on such …
lifecycle of that organism. Various important biological functions are dependent on such …
Prediction of DNA-binding residues in local segments of protein sequences with fuzzy cognitive maps
While protein-DNA interactions are crucial for a wide range of cellular functions, only a small
fraction of these interactions was annotated to date. One solution to close this annotation …
fraction of these interactions was annotated to date. One solution to close this annotation …
Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome
As more and more protein sequences are uncovered from increasingly inexpensive
sequencing techniques, an urgent task is to find their functions. This work presents a highly …
sequencing techniques, an urgent task is to find their functions. This work presents a highly …