Comparative Performance of High-Throughput Methods for Protein pKa Predictions
The medically relevant field of protein-based therapeutics has triggered a demand for
protein engineering in different pH environments of biological relevance. In silico …
protein engineering in different pH environments of biological relevance. In silico …
Predicting positions of bridging water molecules in nucleic acid–ligand complexes
W Wei, J Luo, J Waldispühl… - Journal of Chemical …, 2019 - ACS Publications
Over the past two decades, interests in DNA and RNA as drug targets have been growing
rapidly. Following the trends observed with protein drug targets, computational approaches …
rapidly. Following the trends observed with protein drug targets, computational approaches …
Torsional energy barriers of biaryls could be predicted by electron richness/deficiency of aromatic rings; advancement of molecular mechanics toward atom-type …
Biaryl molecules are ubiquitous pharmacophores found in natural products and
pharmaceuticals. In spite of this, existing molecular mechanics force fields are unable to …
pharmaceuticals. In spite of this, existing molecular mechanics force fields are unable to …
A unique activation–promotion mechanism of the influenza B M2 proton channel uncovered by multiscale simulations
Y Zhang, H Zhang, Q Zheng - Physical Chemistry Chemical Physics, 2019 - pubs.rsc.org
The influenza B M2 protein (BM2) forms an acid-activated proton channel that is important
for the virus's lifecycle. Despite extensive research efforts, the detailed activation mechanism …
for the virus's lifecycle. Despite extensive research efforts, the detailed activation mechanism …
Enzymatic Post-Transfer Editing Mechanism of E. coli Threonyl-tRNA Synthetase (ThrRS): A Molecular Dynamics (MD) and Quantum Mechanics/Molecular …
MM Aboelnga, JJ Hayward, JW Gauld - ACS Catalysis, 2017 - ACS Publications
Threonyl-tRNA synthetase (ThrRS) is a class II aminoacyl-tRNA synthetase (aaRS), which
are a ubiquitous family of enzymes that have a vital role in protein biosynthesis. In particular …
are a ubiquitous family of enzymes that have a vital role in protein biosynthesis. In particular …
Semi-Empirical Born–Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package
Semi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO)
family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By …
family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By …
Fundamentals behind the specificity of Cysteinyl‐tRNA synthetase: MD and QM/MM joint investigations
Cysteinyl‐tRNA synthetase (CysRS) catalyzes the aminoacylation reaction of cysteine to its
cognate tRNACys in the first step of protein translation. It is found that CysRS is different from …
cognate tRNACys in the first step of protein translation. It is found that CysRS is different from …
Threonyl tRNA synthetases as antibiotic targets and resistance mechanisms
J Liston - 2022 - ueaeprints.uea.ac.uk
Threonyl tRNA synthetases (ThrRSs) catalyse the attachment of L-threonine to its cognate
tRNAThr. These enzymes are essential for the translation of proteins. There are currently two …
tRNAThr. These enzymes are essential for the translation of proteins. There are currently two …