Mapping the binding sites of challenging drug targets
An increasing number of medically important proteins are challenging drug targets because
their binding sites are too shallow or too polar, are cryptic and thus not detectable without a …
their binding sites are too shallow or too polar, are cryptic and thus not detectable without a …
[HTML][HTML] Cell phenotypes can be predicted from propensities of protein conformations
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities
of the conformations can be predictors of cell function. The conformational states that the …
of the conformations can be predictors of cell function. The conformational states that the …
Predicting allosteric pockets in protein biological assemblages
Motivation Allostery enables changes to the dynamic behavior of a protein at distant
positions induced by binding. Here, we present APOP, a new allosteric pocket prediction …
positions induced by binding. Here, we present APOP, a new allosteric pocket prediction …
Practical Guidance for Consensus Scoring and Force Field Selection in Protein–Ligand Binding Free Energy Simulations
The advances in ligand binding affinity prediction have been fostered by system generation
tools and improved force fields (FFs). CHARMM-GUI Free Energy Calculator provides input …
tools and improved force fields (FFs). CHARMM-GUI Free Energy Calculator provides input …
Single-Molecule Human Nucleosome Spontaneously Ruptures under the Stress of Compressive Force: A New Perspective on Gene Stability and Epigenetic …
L Shahu, SR Chowdhury, HP Lu - The Journal of Physical …, 2022 - ACS Publications
Force manipulation on the biological entities from living cells to protein molecules has
revealed many mechanical details of cell biology from resolving folding and unfolding …
revealed many mechanical details of cell biology from resolving folding and unfolding …
Gauging Dynamics-driven Allostery Using a New Computational Tool: A CAP Case Study
AP Kornev, JH Weng, RA Maillard, SS Taylor - Journal of molecular biology, 2024 - Elsevier
In this study, we utilize Protein Residue Networks (PRNs), constructed using Local Spatial
Pattern (LSP) alignment, to explore the dynamic behavior of Catabolite Activator Protein …
Pattern (LSP) alignment, to explore the dynamic behavior of Catabolite Activator Protein …
Molecular Simulations of Unexplored Philippine Plant Constituents on the Inhibition of the Proinflammatory Marker NF-κB p50 Subunit
Inflammation serves as a pivotal defense mechanism orchestrated by the innate immune
system to safeguard cellular health against adversities. Nonetheless, dysregulated …
system to safeguard cellular health against adversities. Nonetheless, dysregulated …
From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes?
LF Piochi, AT Gaspar, N Rosário-Ferreira… - Advances in Protein …, 2022 - Elsevier
Cells suffer from perturbations by different stimuli, which, consequently, rise to individual
alterations in their profile and function that may end up affecting the tissue as a whole. This …
alterations in their profile and function that may end up affecting the tissue as a whole. This …
Dynamics-based protein network features accurately discriminate neutral and rheostat positions
In some proteins, a unique class of nonconserved positions is characterized by their ability
to generate diverse functional outcomes through single amino acid substitutions. Due to …
to generate diverse functional outcomes through single amino acid substitutions. Due to …
Dynamic play between human N-α-acetyltransferase D and H4-mutant histones: Molecular dynamics study
SB Rathod, KR Srivastava - Current Protein and Peptide …, 2023 - ingentaconnect.com
Background: Many N-terminal acetyltransferases (NATs) play important role in the
posttranslational modifications of histone tails. Research showed that these enzymes have …
posttranslational modifications of histone tails. Research showed that these enzymes have …