• Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents

    25 days ago - By IEEE/ACM

    The novel SARS-CoV-2 uses ACE2 receptor as an entry point. Insights on S protein receptor-binding domain interaction with ACE2 receptor and drug repurposing has accelerated drug discovery for the novel SARS-CoV-2 infection. Finding small molecule binding sites in S protein and ACE2 interface is crucial in search of effective drugs to prevent viral entry. In this study, we employed molecular dynamics simulations in mixed solvents together with virtual screening to identify small molecules that could be potential inhibitors of S protein -ACE2 interaction. Observation of organic probe...
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  • On the Use of Intra‐Molecular Distance and Angle Constraints to Lengthen the Time Step in Molecular and Stochastic Dynamics Simulations of Proteins

    25 days ago - By Wiley

    Abstract
    Computer simulation of proteins in aqueous solution at the atomic level of resolution is still limited in time span and system size due to limited computing power available and thus employs a variety of time-saving techniques that trade some accuracy against computational effort. An example of such a time-saving technique is the application of constraints to particular degrees of freedom when integrating Newton's or Langevin's equations of motion in molecular dynamics or stochastic dynamics simulations, respectively. The application of bond-length constraints is standard practice...
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