Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Molecular determinants of drug–receptor binding kinetics
It is increasingly appreciated that the rates at which drugs associate with and dissociate from
receptors—the binding kinetics—directly impact drug efficacy and safety. The molecular …
receptors—the binding kinetics—directly impact drug efficacy and safety. The molecular …
Molecular dynamics simulations for rationalizing polymer bioconjugation strategies: Challenges, recent developments, and future opportunities
J Kehrein, C Sotriffer - ACS Biomaterials Science & Engineering, 2023 - ACS Publications
The covalent modification of proteins with polymers is a well-established method for
improving the pharmacokinetic properties of therapeutically valuable biologics. The …
improving the pharmacokinetic properties of therapeutically valuable biologics. The …
Modeling protein association mechanisms and kinetics
Highlights•Protein association rate constants are essential for cellular functions.•Half of the
problem of modeling association kinetics has a solution.•Binding of disordered proteins …
problem of modeling association kinetics has a solution.•Binding of disordered proteins …
Modeling crowded environment in molecular simulations
Biomolecules perform their various functions in living cells, namely in an environment that is
crowded by many macromolecules. Thus, simulating the dynamics and interactions of …
crowded by many macromolecules. Thus, simulating the dynamics and interactions of …
Ligand binding pathways and conformational transitions of the HIV protease
It is important to determine the binding pathways and mechanisms of ligand molecules to
target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a …
target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a …
[PDF][PDF] Docking and ligand binding affinity: uses and pitfalls
MJR Yunta - Am. J. Model. Optim, 2016 - researchgate.net
In this review article, we will explore the foundations of different classes of docking and
scoring functions, their possible limitations, and their suitable application domains. We also …
scoring functions, their possible limitations, and their suitable application domains. We also …
Escape of a small molecule from inside T4 lysozyme by multiple pathways
Abstract The T4 lysozyme L99A mutant is often used as a model system to study small-
molecule binding to proteins, but pathways for ligand entry and exit from the buried binding …
molecule binding to proteins, but pathways for ligand entry and exit from the buried binding …
Molecular modelling and simulations in cancer research
R Friedman, K Boye, K Flatmark - … et Biophysica Acta (BBA)-Reviews on …, 2013 - Elsevier
The complexity of cancer and the vast amount of experimental data available have made
computer-aided approaches necessary. Biomolecular modelling techniques are becoming …
computer-aided approaches necessary. Biomolecular modelling techniques are becoming …
Effects of macromolecular crowding on the conformational ensembles of disordered proteins
Due to their conformational malleability, intrinsically disordered proteins (IDPs) are
particularly susceptible to influences of crowded cellular environments. Here we report a …
particularly susceptible to influences of crowded cellular environments. Here we report a …