QM/MM free energy simulations: recent progress and challenges
Due to the higher computational cost relative to pure molecular mechanical (MM)
simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy …
simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy …
Discovery and mining of enzymes from the human gut microbiome
Advances in technological and bioinformatics approaches have led to the generation of a
plethora of human gut metagenomic datasets. Metabolomics has also provided substantial …
plethora of human gut metagenomic datasets. Metabolomics has also provided substantial …
Perspective: Quantum mechanical methods in biochemistry and biophysics
Q Cui - The Journal of chemical physics, 2016 - pubs.aip.org
In this perspective article, I discuss several research topics relevant to quantum mechanical
(QM) methods in biophysical and biochemical applications. Due to the immense complexity …
(QM) methods in biophysical and biochemical applications. Due to the immense complexity …
[PDF][PDF] Confronting the catalytic dark matter encoded by sequenced genomes
The post-genomic era has provided researchers with a deluge of protein sequences.
However, a significant fraction of the proteins encoded by sequenced genomes remains …
However, a significant fraction of the proteins encoded by sequenced genomes remains …
Machine learning enables prediction of Pyrrolysyl-tRNA synthetase substrate specificity
Knowledge about the substrate scope for a given enzyme is informative for elucidating
biochemical pathways and also for expanding applications of the enzyme. However, no …
biochemical pathways and also for expanding applications of the enzyme. However, no …
[HTML][HTML] PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking
Plant cytochrome P450s play key roles in the diversification and functional modification of
plant natural products. Although over 200,000 plant P450 gene sequences have been …
plant natural products. Although over 200,000 plant P450 gene sequences have been …
Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex
N Pinotsis, A Krüger, N Tomas… - Nature …, 2023 - nature.com
The identification and characterization of enzyme function is largely lacking behind the
rapidly increasing availability of large numbers of sequences and associated high-resolution …
rapidly increasing availability of large numbers of sequences and associated high-resolution …
Machine learning‐based prediction of enzyme substrate scope: application to bacterial nitrilases
Z Mou, J Eakes, CJ Cooper, CM Foster… - Proteins: Structure …, 2021 - Wiley Online Library
Predicting the range of substrates accepted by an enzyme from its amino acid sequence is
challenging. Although sequence‐and structure‐based annotation approaches are often …
challenging. Although sequence‐and structure‐based annotation approaches are often …
Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering
M Da Costa, O Gevaert, S Van Overtveldt, J Lange… - Biotechnology …, 2021 - Elsevier
Abstract Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide
sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare …
sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare …
Regulation and plasticity of catalysis in enzymes: insights from analysis of mechanochemical coupling in myosin
The mechanism of ATP hydrolysis in the myosin motor domain is analyzed using a
combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The …
combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The …