Molecular simulations, {including|such as|which includes|like} quantum mechanics (QM), molecular mechanics (MM), and multiscale QM/MM modeling, {have been|happen to be|have already been} extensively applied {to understand|to know} the mechanism of enzyme catalysis and to {design|style|design and style} new enzymes. {However|Nevertheless|Nonetheless|Even so|On the other hand|Having said that}, molecular simulations {typically|usually|normally|generally|commonly|ordinarily} {require|need|demand|call for} specialized, manual operation ranging from model {construction|building} to post-analysis {to complete|to finish} {the entire|the whole|the complete} life-cycle of enzyme modeling. The dependence on manual operation {makes|tends to make} it {challenging|difficult} to simulate enzymes and enzyme variants {in a|inside a|within a} high-throughput {fashion|style}. {In this|Within this} {work|function|perform|operate}, we {developed|created} a Python {software|software program|computer software|application}, EnzyHTP, to automate molecular model {construction|building}, QM, MM, and QM/MM computation, and analyses of modeling {data|information} for enzyme simulations. To test the EnzyHTP, we {used|utilized|employed|utilised|applied|made use of} fluoroacetate dehalogenase (FAcD) as a model {system|method|program|technique} and simulated the enzyme interior electrostatics for {100|one hundred} FAcD mutants {with a|having a|using a} random single amino acid substitution. For {each|every|each and every|every single} enzyme mutant, the workflow {involves|entails|requires|includes} structural model {construction|building}, 1 ns molecular dynamics simulations, and quantum mechnical calculations in {100|one hundred} MD-sampled snapshots. {The entire|The whole|The complete} simulation workflow for {100|one hundred} mutants was completed in 7 hours with {10|ten} GPUs and 160 CPUs. EnzyHTP is {expected|anticipated} {to improve|to enhance} the efficiency and reproducibility of computational enzyme, facilitate the {fundamental|basic} understanding of catalytic origins across enzyme {families|households}, and accelerate the optimization of biocatalysts for non-native substrate transformation. Price of 27194-74-7 1196153-26-0 manufacturer PMID:23771862
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