Given the overall similarities between protein folding and RNA folding, and between protein-protein binding and protein–nucleic acid binding, we reasoned that the concepts and techniques underlying AlphaFold and RoseTTAFold could be extended to the prediction of the structures of nucleic acids and ...
We anticipate that this type of approach could be used for the design of interfaces, protein–nucleic acid complexes, and ligand binding sites. Notably, the design algorithm reflects key characteristics of energy functions, such as the ability to (1) accurately determine side-chain conformations, ...
As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. ...
The third experiment involves evaluating the learning capacity of xCAPT5 on more constrained datasets with different stringent similarities in sequences. Chen’s multispecies dataset [3] is used, with stringent similarity values ranging from 0.01 to 0.4. The performance of the models is evaluated usin...
In 1873 a Dutch physicist Johannes Diderik van der Waals, postulated the intermolecular forces are necessary for the real gases. It is as important as other forces for the structure protein–ligand, protein-protein, and nucleic acid–ligand interactions etc. Both attractive and repulsive van der ...
A heme structure is bound in many globin fold proteins that binds and carries oxygen in an organism. The globin fold structure has been preserved in mammals, insects, and plants although the amino acid sequence similarities may be very low between such disparate species. Thus, natural selection ...
Protein biosynthesis at the ribosome results in the conversion of nucleic acid genetic information into the polypeptides essential for cellular function. Peptide bond formation requires numerous protein and nucleotide cofactors in addition to the ribosome itself, and is tightly regulated to ensure accurate...
To this end, we analysed a set of 53507 homology models that cover the whole sequence identity range, with a special emphasis on medium and low similarities. More precisely we examined how cleft quality – measured using six complementary parameters related to both global shape and local atomic ...
1c). The plDDT scores are high for a range of different conformations and similarities to both train and test conformations vary extensively. There seems to be no clear relationship between the plDDT and known conformations from the PDB suggesting that confidence metrics can’t be used to ...
Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individua