Artificial intelligence-based protein structure prediction approaches have had a transformative effect on biomolecular sciences. The predicted protein models in the AlphaFold protein structure database, however, all lack coordinates for small molecules, essential for molecular structure or function: hemoglobin...
For example, an analysis of the CATH database of fold structures showed that 98.8 % of the folds fall into the correct CATH homologous superfamily category, based on the highest PRIDE score obtained. Structural alignment and secondary-structure assignment are not necessary for the calculation of ...
For sake of scoring the methods on the same protein, we performed a side-by-side comparison of AlphaFold2 and ESMFold models and obtained the scatter plot of Figure 1. Here, we group data by considering the TM-score difference of both models with respect to the corresponding PDB structure ...
α/βHydrolase Fold: An Update Alpha/beta hydrolase fold: an update. Protein Peptide Lett. 16:1137-1148.Carr PD, Ollis DL (2009). Alpha/beta hydrolase fold: an update. Protein ... David,L.,Ollis,... - 《Protein & Peptide Letters》 被引量: 151发表: 2009年 ESTHER, the database of...
Letter to the Editor: Solution structure of the hypothetical protein MTH0637 from Methanobacterium thermoautotrophicum Valencia A, Arrowsmith CH, Rico M: Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold... A Pineda-Lucena,GS Yi,...
Here we describe the design and development of the Alphabody, a protein scaffold featuring a single-chain antiparallel triple-helix coiled-coil fold. We report affinity-matured Alphabodies with favourable physicochemical properties that can specifically neutralize human interleukin (IL)-23, a pivotal ...
AlphaFold Multimer is an extension of AlphaFold2 that has been specifically built to predict protein-protein complexes. Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accura...
A protein fold for this domain is proposed to correspond to a doubly-wound open twisted beta-sheet structure flanked by alpha-helices. Close agreement was found with the GTP-binding domain of human ras-p21, provided that an extra alpha-helix was inserted. The structure of the predicted fold ...
The RNA-binding surface of the SAM domain is structurally equivalent to the DNA-binding surface of the Holliday-junction-binding protein, RuvA, which shares the SAM-like protein fold and binds DNA (SCOP database). Thus, the SAM-like domain can be used to interact with protein, DNA or RNA...
(Note that this assumption is not always valid and can be restricted to certain protein classes). In the second step, adjusted intensities are derived for each protein, such that protein intensities between different MS runs can be compared. To this end, we derive the median peptide fold ...