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 …
Along the allostery stream: Recent advances in computational methods for allosteric drug discovery
Allostery is a universal, biological phenomenon in which orthosteric sites are fine‐tuned by
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …
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 …
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 …
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 …
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the
current COVID-19 pandemic that is severely damaging global health and the economy …
current COVID-19 pandemic that is severely damaging global health and the economy …
[HTML][HTML] Protein dynamics underlying allosteric regulation
Allostery is the mechanism by which information and control are propagated in
biomolecules. It regulates ligand binding, chemical reactions, and conformational changes …
biomolecules. It regulates ligand binding, chemical reactions, and conformational changes …
Identification of cryptic binding sites using MixMD with standard and accelerated molecular dynamics
RD Smith, HA Carlson - Journal of chemical information and …, 2021 - ACS Publications
Protein dynamics play an important role in small molecule binding and can pose a
significant challenge in the identification of potential binding sites. Cryptic binding sites have …
significant challenge in the identification of potential binding sites. Cryptic binding sites have …
AlphaFold meets flow matching for generating protein ensembles
The biological functions of proteins often depend on dynamic structural ensembles. In this
work, we develop a flow-based generative modeling approach for learning and sampling the …
work, we develop a flow-based generative modeling approach for learning and sampling the …