Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.9b00635
Abstract: Splicing modulators (SMs) pladienolides, herboxidienes and spliceostatins exert their antitumor activity by altering the ability of SF3B1 and PHF5A proteins, components of SF3b splicing factor, to recognize distinct intron branching point sequences, thus finely calibrating… read more here.
Keywords: structural information; sf3b1; cryo structural; information ... See more keywords
Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c00016
Abstract: Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG force fields to match all-atom simulations has mainly relied on force-matching… read more here.
Keywords: flow matching; efficient coarse; force matching; matching efficient ... See more keywords
All-Atom Simulations Decrypt the Molecular Terms of RNA Catalysis in the Exon-Ligation Step of the Spliceosome
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DOI: 10.1021/acscatal.0c00390
Abstract: The spliceosome, a protein-directed metallo-ribozyme, catalyzes premature mRNA splicing via two transesterification reactions. The atomic-level details of the splicing mechanism and the role of the... read more here.
Keywords: simulations decrypt; terms rna; molecular terms; catalysis ... See more keywords
All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery
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DOI: 10.3390/v13040564
Abstract: The hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130,… read more here.
Keywords: simulations hbv; hbv capsid; atom simulations; reveal ... See more keywords