Results 51 to 60 of about 1,488,373 (296)

DBSI: DNA-binding site identifier [PDF]

Nucleic Acids Research, 2013
In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30 ...
Zhu, Xiaolei, Ericksen, Spencer S., Mitchell, Julie C.   +2 more
openaire   +2 more sources

Peptide‐based ligand antagonists block a Vibrio cholerae adhesin

FEBS Letters, EarlyView.
The structure of a peptide‐binding domain of the Vibrio cholerae adhesin FrhA was solved by X‐ray crystallography, revealing how the inhibitory peptide AGYTD binds tightly at its Ca2+‐coordinated pocket. Structure‐guided design incorporating D‐amino acids enhanced binding affinity, providing a foundation for developing anti‐adhesion therapeutics ...
Mingyu Wang, Grace Du, Charity Yongo‐Luwawa, Angelina Lu, Brett Kinrade, Kim Munro, Karl E. Klose, William D. Lubell, Peter Davies, Shuaiqi Guo   +9 more
wiley   +1 more source

c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. [PDF]

PLoS ONE, 2015
Strict control of tissue-specific gene expression plays a pivotal role during lineage commitment. The transcription factor c-Myb has an essential role in adult haematopoiesis and functions as an oncogene when rearranged in human cancers.
Mads Bengtsen, Kjetil Klepper, Sveinung Gundersen, Ignacio Cuervo, Finn Drabløs, Eivind Hovig, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland   +8 more
doaj   +1 more source

Unique MAP Kinase binding sites [PDF]

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2008
Map kinases are drug targets for autoimmune disease, cancer, and apoptosis-related diseases. Drug discovery efforts have developed MAP kinase inhibitors directed toward the ATP binding site and neighboring "DFG-out" site, both of which are targets for inhibitors of other protein kinases.
Radha, Akella, Thomas M, Moon, Elizabeth J, Goldsmith   +2 more
openaire   +2 more sources

Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

FEBS Letters, EarlyView.
This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley   +1 more source

Polyphenol Interactions with Amyloid Fibrils: A Molecular Docking Study

East European Journal of Physics
Polyphenols, a versatile group of naturally occurring compounds with many favorable biological properties currently attract increasing research interest in the context of their ability to inhibit the formation and to destabilize special protein ...
Uliana Malovytsia, Valeriya Trusova, Mette Thomsen, Kateryna Vus, Olga Zhytniakivska, Galyna Gorbenko   +5 more
doaj   +1 more source

Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision

Journal of Cheminformatics, 2021
Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based discovery of novel drug candidates.
Merveille Eguida, Didier Rognan
doaj   +1 more source

Real‐time assay of ribonucleotide reductase activity with a fluorescent RNA aptamer

FEBS Letters, EarlyView.
Ribonucleotide reductases (RNR) synthesize DNA building blocks de novo, making them crucial in DNA replication and drug targeting. FLARE introduces the first single‐tube real‐time coupled RNR assay, which enables isothermal tracking of RNR activity at nanomolar enzyme levels and allows the reconstruction of allosteric regulatory patterns and rapid ...
Jacopo De Capitani, Noemi E. Nwosu, Viktoria Gocke, Müge Kasanmascheff, Hannes Mutschler   +4 more
wiley   +1 more source

Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing

FEBS Letters, EarlyView.
Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley   +1 more source

Structural Analysis of the Drosophila melanogaster GSTome

Biomolecules
Glutathione transferase (GST) is a superfamily of ubiquitous enzymes, multigenic in numerous organisms and which generally present homodimeric structures.
Nicolas Petiot, Mathieu Schwartz, Patrice Delarue, Patrick Senet, Fabrice Neiers, Adrien Nicolaï   +5 more
doaj   +1 more source