Markov state models: From an art to a science
Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …
could provide reliable answers to questions pertaining to the structure-function relationship …
SARS-CoV-2 simulations go exascale to capture spike opening and reveal cryptic pockets across the proteome
MI Zimmerman, G Bowman - Biophysical Journal, 2021 - cell.com
The SARS-CoV-2/COVID-19 pandemic continues to threaten global health and
socioeconomic stability. Experiments have revealed snapshots of many viral components …
socioeconomic stability. Experiments have revealed snapshots of many viral components …
Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain
HC Feldman, E Merlini, C Guijas… - Proceedings of the …, 2022 - National Acad Sciences
The nicotinamide adenine dinucleotide hydrolase (NADase) sterile alpha toll/interleukin
receptor motif containing-1 (SARM1) acts as a central executioner of programmed axon …
receptor motif containing-1 (SARM1) acts as a central executioner of programmed axon …
Accelerating cryptic pocket discovery using AlphaFold
Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold
great potential as drug targets. However, cryptic pocket openings are often beyond the reach …
great potential as drug targets. However, cryptic pocket openings are often beyond the reach …
Crossroads of antibiotic resistance and biosynthesis
TA Wencewicz - Journal of molecular biology, 2019 - Elsevier
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic
producers are an integral part of the growing antibiotic resistance threat. The origins of …
producers are an integral part of the growing antibiotic resistance threat. The origins of …
Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network
Cryptic pockets expand the scope of drug discovery by enabling targeting of proteins
currently considered undruggable because they lack pockets in their ground state structures …
currently considered undruggable because they lack pockets in their ground state structures …
Investigating cryptic binding sites by molecular dynamics simulations
A Kuzmanic, GR Bowman… - Accounts of chemical …, 2020 - ACS Publications
Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains
The design of compounds that can discriminate between closely related target proteins
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …
Folding@ home: Achievements from over 20 years of citizen science herald the exascale era
Simulations of biomolecules have enormous potential to inform our understanding of biology
but require extremely demanding calculations. For over 20 years, the Folding@ home …
but require extremely demanding calculations. For over 20 years, the Folding@ home …