Chemical complexity challenge: Is multi‐instance machine learning a solution?
Molecules are complex dynamic objects that can exist in different molecular forms
(conformations, tautomers, stereoisomers, protonation states, etc.) and often it is not known …
(conformations, tautomers, stereoisomers, protonation states, etc.) and often it is not known …
DNA–protein interaction studies: a historical and comparative analysis
RAC Ferraz, ALG Lopes, JAF da Silva, DFV Moreira… - Plant Methods, 2021 - Springer
DNA–protein interactions are essential for several molecular and cellular mechanisms, such
as transcription, transcriptional regulation, DNA modifications, among others. For many …
as transcription, transcriptional regulation, DNA modifications, among others. For many …
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins
Current predictors of DNA-binding residues (DBRs) from protein sequences belong to two
distinct groups, those trained on binding annotations extracted from structured protein-DNA …
distinct groups, those trained on binding annotations extracted from structured protein-DNA …
A deep learning-based method for the prediction of DNA interacting residues in a protein
S Patiyal, A Dhall, GPS Raghava - Briefings in Bioinformatics, 2022 - academic.oup.com
DNA–protein interaction is one of the most crucial interactions in the biological system,
which decides the fate of many processes such as transcription, regulation and splicing of …
which decides the fate of many processes such as transcription, regulation and splicing of …
Protein–nucleic acid interactions for RNA polymerase II elongation factors by molecular dynamics simulations
A Gallardo, BM Bogart, B Dutagaci - Journal of Chemical …, 2022 - ACS Publications
RNA polymerase II (Pol II) forms a complex with elongation factors to proceed to the
elongation stage of the transcription process. In this work, we studied the elongation factor …
elongation stage of the transcription process. In this work, we studied the elongation factor …
Lambda CI binding to related phage operator sequences validates alignment algorithm and highlights the importance of overlooked bonds
J Sedhom, LA Solomon - Genes, 2023 - mdpi.com
Bacteriophage λ's CI repressor protein controls a genetic switch between the virus's
lysogenic and lytic lifecycles, in part, by selectively binding to six different DNA sequences …
lysogenic and lytic lifecycles, in part, by selectively binding to six different DNA sequences …
qNABpredict: Quick, accurate, and taxonomy‐aware sequence‐based prediction of content of nucleic acid binding amino acids
Protein sequence‐based predictors of nucleic acid (NA)‐binding include methods that
predict NA‐binding proteins and NA‐binding residues. The residue‐level tools produce …
predict NA‐binding proteins and NA‐binding residues. The residue‐level tools produce …
DBpred: A deep learning method for the prediction of DNA interacting residues in protein sequences
S Patiyal, A Dhall, GPS Raghava - BioRxiv, 2021 - biorxiv.org
DNA-protein interaction is one of the most crucial interactions in the biological system, which
decide the fate of many processes such as transcription, regulation of gene expression …
decide the fate of many processes such as transcription, regulation of gene expression …
Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein
J Sedhom, J Kinser, LA Solomon - NAR Genomics and …, 2022 - academic.oup.com
Protein–DNA binding is of a great interest due to its importance in many biological
processes. Previous studies have presented many factors responsible for the recognition …
processes. Previous studies have presented many factors responsible for the recognition …
Discovery of Virus-Host interactions using bioinformatic tools
C Marques-Pereira, M Pires, IS Moreira - Methods in Cell Biology, 2022 - Elsevier
Viruses are a diverse biological group capable of infecting several hosts such as bacteria,
plants, and animals, including humans. Viral infections constitute a threat to the human …
plants, and animals, including humans. Viral infections constitute a threat to the human …