Διαφάνειες διαλέξεων, βιβλιογραφία και ανακοινώσεις
Hands-on workshop
Paxlovid is the latest COVID-19 treatment that’s been all over the news. The drug was granted an emergency use authorization (EUA) by the Food and Drug Administration (FDA) in December for anyone ages 12 and older who weighs at least 88 pounds, and is at high risk for severe disease. Paxlovid is an active 3Cl protease inhibitor. Paxlovid exerts its antiviral efficacy by inhibiting a necessary protease in the viral replication procedure.
To video με την διαδικασία docking με το Autodock (YouTube)
Τα μόρια για το παράδειγμα με το Autodock (αρχείο zip)
Ασκήσεις
Εργασία #1. Ημερομηνία παράδοσης 21/11/24
Εργασία #2. Ημερομηνία παράδοσης 28/11/24
Misc Resources
Computational Methods for Drug Discovery and Design — The Journal of Chemical Information and Modeling and the Journal of Medicinal Chemistry are pleased to introduce a joint Virtual Issue on computational methods for drug discovery and design.
Computational Methods for Medicinal Chemistry Collection — A thematic collection of articles selected from the Journal of Medicinal Chemistry has been created that highlights computational methods and workflows relevant for the practice of medicinal chemistry.
Protein Fluctuations and Cavity Changes Relationship — Protein cavities and tunnels are critical for function. Ligand recognition and binding, transport, and enzyme catalysis require cavities rearrangements. Therefore, the flexibility of cavities should be guaranteed by protein vibrational dynamics. Molecular dynamics simulations provide a framework to explore conformational plasticity of protein cavities. Herein, we present a novel procedure to characterize the dynamics of protein cavities in terms of their volume gradient vector. For this purpose, we make use of algorithms for calculation of the cavity volume that result robust for numerical differentiations. Volume gradient vector is expressed in terms of principal component analysis obtained from equilibrated molecular dynamics simulations. We analyze contributions of principal component modes to the volume gradient vector according to their frequency and degree of delocalization. In all our test cases, we find that low frequency modes play a critical role together with minor contributions of high frequency modes. These modes involve concerted motions of significant fractions of the total residues lining the cavities. We make use of variations of the potential energy of a protein in the direction of the volume gradient vector as a measure of flexibility of the cavity. We show that proteins whose collective low frequency fluctuations contribute the most to changes of cavity volume exhibit more flexible cavities.
Using AutoDock 4 and AutoDock Vina with AutoDockTools — A Tutorial Written by Ruth Huey, Garrett M. Morris and Stefano Forli The Scripps Research Institute Molecular Graphics Laboratory 10550 N. Torrey Pines Rd. La Jolla, California 92037-1000 USA