Docking techniques in toxicology: an overview
A variety of environmental toxicants such as heavy metals, pesticides, organic chemicals, etc
produce harmful effects in our living systems. In the literature, various reports have indicated …
produce harmful effects in our living systems. In the literature, various reports have indicated …
[HTML][HTML] Protein-DNA docking with a coarse-grained force field
P Setny, RP Bahadur, M Zacharias - BMC bioinformatics, 2012 - Springer
Background Protein-DNA interactions are important for many cellular processes, however
structural knowledge for a large fraction of known and putative complexes is still lacking …
structural knowledge for a large fraction of known and putative complexes is still lacking …
[HTML][HTML] The binding of syndapin SH3 domain to dynamin proline-rich domain involves short and long distance elements
Dynamin is a GTPase that mediates vesicle fission during synaptic vesicle endocytosis. Its
long C-terminal proline-rich domain contains 13 PXXP motifs, which orchestrate its …
long C-terminal proline-rich domain contains 13 PXXP motifs, which orchestrate its …
ParaDock: a flexible non-specific DNA—rigid protein docking algorithm
I Banitt, HJ Wolfson - Nucleic Acids Research, 2011 - academic.oup.com
Accurate prediction of protein–DNA complexes could provide an important stepping stone
towards a thorough comprehension of vital intracellular processes. Few attempts were made …
towards a thorough comprehension of vital intracellular processes. Few attempts were made …
Solution structures of the trihelix DNA‐binding domains of the wild‐type and a phosphomimetic mutant of Arabidopsis GT‐1: Mechanism for an increase in DNA …
T Nagata, E Niyada, N Fujimoto… - Proteins: Structure …, 2010 - Wiley Online Library
GT‐1 is a plant transcription factor that binds to one of the cis‐acting elements, BoxII, which
resides within the upstream promoter region of light‐responsive genes. GT‐1 was assumed …
resides within the upstream promoter region of light‐responsive genes. GT‐1 was assumed …
Solution NMR structure of putidaredoxin–cytochrome P450cam complex via a combined residual dipolar coupling–spin labeling approach suggests a role for Trp106 …
The 58-kDa complex formed between the [2Fe–2S] ferredoxin, putidaredoxin (Pdx), and
cytochrome P450cam (CYP101) from the bacterium Pseudomonas putida has been …
cytochrome P450cam (CYP101) from the bacterium Pseudomonas putida has been …
The C-terminal zinc fingers of ZBTB38 are novel selective readers of DNA methylation
A Pozner, NO Hudson, J Trewhella… - Journal of molecular …, 2018 - Elsevier
Methyl-CpG binding proteins play an essential role in translating DNA methylation marks
into a downstream transcriptional response, which has implications for both normal cell …
into a downstream transcriptional response, which has implications for both normal cell …
Targeting tachykinin peptides involved in viral infections through in silico approach: Screening the unforeseen potency of serratiopeptidase
A Dhiman, R Purohit - Journal of Molecular Liquids, 2023 - Elsevier
Viral infections present formidable hurdles to global public health, thus demanding the
imperative development of efficacious therapeutic interventions. In the realm of antiviral …
imperative development of efficacious therapeutic interventions. In the realm of antiviral …
Multiscale modeling of macromolecular biosystems
In this article, we review the recent progress in multiresolution modeling of structure and
dynamics of protein, RNA and their complexes. Many approaches using both physics-based …
dynamics of protein, RNA and their complexes. Many approaches using both physics-based …
[PDF][PDF] The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix-hairpin-helix domains in ss/ds DNA recognition
D Das, GE Folkers, M van Dijk, NGJ Jaspers… - Structure, 2012 - cell.com
Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA
strand at the 5′ end during nucleotide excision repair. We determined the structure of the …
strand at the 5′ end during nucleotide excision repair. We determined the structure of the …