The role of protein loops and linkers in conformational dynamics and allostery
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …
take place on a wide range of time scales. These changes can be as small as the rotation of …
Protein allostery and conformational dynamics
The functions of many proteins are regulated through allostery, whereby effector binding at a
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born
We present an implementation of generalized Born implicit solvent all-atom classical
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …
Optimized molecular dynamics force fields applied to the helix− coil transition of polypeptides
Obtaining the correct balance of secondary structure propensities is a central priority in
protein force-field development. Given that current force fields differ significantly in their α …
protein force-field development. Given that current force fields differ significantly in their α …
Long-timescale molecular dynamics simulations of protein structure and function
JL Klepeis, K Lindorff-Larsen, RO Dror… - Current opinion in …, 2009 - Elsevier
Molecular dynamics simulations allow for atomic-level characterization of biomolecular
processes such as the conformational transitions associated with protein function. The …
processes such as the conformational transitions associated with protein function. The …
Millisecond-scale molecular dynamics simulations on Anton
Anton is a recently completed special-purpose supercomputer designed for molecular
dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware …
dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware …
Integrative, dynamic structural biology at atomic resolution—it's about time
H Van Den Bedem, JS Fraser - Nature methods, 2015 - nature.com
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …
interact with binding partners or perform the chemical reactions required for a multitude of …
Discovery through the computational microscope
All-atom molecular dynamics simulations have become increasingly popular as a tool to
investigate protein function and dynamics. However, researchers are concerned about the …
investigate protein function and dynamics. However, researchers are concerned about the …
Beta-sitosterol attenuates insulin resistance in adipose tissue via IRS-1/Akt mediated insulin signaling in high fat diet and sucrose induced type-2 diabetic rats
In our previous study, we have shown that β-sitosterol (SIT) enhances glycemic control by
increasing the activation of insulin receptor (IR) and glucose transporter 4 (GLUT4) proteins …
increasing the activation of insulin receptor (IR) and glucose transporter 4 (GLUT4) proteins …