Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec a
DynamicBind executes “dynamic docking”, a process that performs prediction of the protein–ligand complex structure while accommodating substantial protein conformational changes. DynamicBind accepts apo-like structures (in the present study, AlphaFold-predicted conformations) in PDB format and small-molecu...
These enzymes are responsible for responding to environmental signals and coordinating cellular responses to ensure growth and survival. STPK-mediated phosphorylation has recently been reported to inhibit many enzymes involved in MA biosynthesis, including proteins involved in MA chain elongation within the...
A reasonable depth of proteomic analysis is needed to ensure a robust contribution of the histone MS signal, but the necessary depth should be readily attainable with many experimental setups. We expect that in the future, more and more proteomics projects will reach the required depth of ...
ensure_n_training_genes.py All scripts (files ending with*.pland*.py) that are part of BRAKER must be executable in order to run BRAKER. This should already be the case if you download BRAKER from GitHub. Executability may be overwritten if you e.g. transfer BRAKER on a USB-stick to...
• Quickly QC protein preps to ensure protein integrity and⁄or purity Two Kits to Choose From The Protein Thermal Shift™ Dye Kit contains the dye and buffer for performing protein thermal shift experiments, enough for up to 1000 reactions. The Protein Thermal Shift™ Starter Kit contains...
Protein carbamylation is of great concern both in vivo and in vitro. Here, we report the first structural characterization of a protein carbamylated at the N-terminal proline. The unexpected carbamylation of the a-amino group of the least reactive codified amino acid has been detected in high-...
Proteins with two or more unique peptides were filtered to ensure that they were detected in at least 2/3 replicates of EV or WCL for the yeast strains and 4/5 replicates of EV or WCL for the biofilm strain. EV proteins remain- ing post-filtering ranged from 690 in DAY286 yeast EVs ...
Despite breakthroughs achieved in protein sequence-to-structure and function-to-sequence predictions, the affinity-to-mutation prediction problem remains unsolved. Such a problem is of exponential complexity deemed to find a mutated protein or protein co
in a T-1-P Laboratory continuous flow centrifuge (Sharples) and resuspended in 1 mL S30A buffer per gram of cell pellet. The resuspended cells were run through an M110-EH-30 microfluidizer (Microfluidics Corp.) at 20,000 PSI twice to ensure complete lysis. The lysate was clarified by ...