Computational tools for aptamer identification and optimization
D Sun, M Sun, J Zhang, X Lin, Y Zhang, F Lin… - TrAC Trends in …, 2022 - Elsevier
Aptamers are single-stranded DNA or RNA oligonucleotides that can selectively bind to a
specific target. They are generally obtained by SELEX, but the procedure is challenging and …
specific target. They are generally obtained by SELEX, but the procedure is challenging and …
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
High‐resolution experimental structural determination of protein–protein interactions has led
to valuable mechanistic insights, yet due to the massive number of interactions and …
to valuable mechanistic insights, yet due to the massive number of interactions and …
[PDF][PDF] ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation
Summary ATG9A and ATG2A are essential core members of the autophagy machinery.
ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer …
ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer …
The evolution of paramagnetic NMR as a tool in structural biology
Paramagnetic NMR data contain extremely accurate long-range information on
metalloprotein structures and, when used in the frame of integrative structural biology …
metalloprotein structures and, when used in the frame of integrative structural biology …
Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling
ZC Drake, JT Seffernick, S Lindert - Nature communications, 2022 - nature.com
Covalent labeling (CL) in combination with mass spectrometry can be used as an analytical
tool to study and determine structural properties of protein-protein complexes. However …
tool to study and determine structural properties of protein-protein complexes. However …
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus
FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural
folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking …
folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking …
Identification of potential inhibitors for LLM of Staphylococcus aureus: structure-based pharmacophore modeling, molecular dynamics, and binding free energy …
Staphylococcus aureus causes various life-threatening diseases in humans and developed
resistance to several antibiotics. Lipophilic membrane (LLM) protein regulates bacterial lysis …
resistance to several antibiotics. Lipophilic membrane (LLM) protein regulates bacterial lysis …
In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target
Klebsiella pneumonia is known to cause several nosocomial infections in
immunocompromised patients. It has developed resistance against a broad range of …
immunocompromised patients. It has developed resistance against a broad range of …
Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2
Abstract The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome
coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with …
coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with …
Protein–protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics
Protein–protein interactions (PPIs) play key roles in many fundamental biological processes
such as cellular signaling and immune responses. However, it has proven challenging to …
such as cellular signaling and immune responses. However, it has proven challenging to …