protein stabilityA structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native...
To address this question, we compared generated sequences from CoVES against sequences designed from two models that can consider the sequence context in an autoregressive manner (proteinMPNN from Dauparas et al.24, Ingraham et al.25; ESM-IF from Hsu et al.8). The high predictive accuracy o...
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust p
structure based drug design such as in silico screening;because based on these representative structures the three-dimensional structures of the remaining proteins encoded in the various genomes can be predicted by homology modeling.The results of the last Critical Assessment of Techniques for Protein ...
MAP(2.0)3D: a sequence/structure based server for protein engineering. Verma R, Schwaneberg U, Roccatano D (2012) MAP2.03D: a sequence/structure based server for protein engineering. ACS Synth Biol 1(4):139-150... R Verma,U Schwaneberg,D Roccatano - 《Acs Synthetic Biology》 被引量...
Figure 4, taken from the protein data bank (PDB 2HY9), illustrates the G-quadruplex structure of the telomere sequence in vertebrates. Table 4. Group analysis of the telomere sequence found in some eukaryotes. The first column is for the telomere repeat, the second column is the organism un...
(C). Secondary structure predictions are a set of approaches in the field of bioinformatics that assist to identify and characterize the secondary configurations of proteinsequences based on their primary structures (Rashid et al., 2016). The earlier methods of structure predictions, in the year ...
Particular attention should be paid to the protein construct, since minor changes to the amino-acid sequence can have a dramatic influence on the solubility, stability, and crystallization behavior. De novo crystallization. Obtaining X-ray quality crystals is usually the most difficult and time-...
Structure prediction of protein-ligand complexes from sequence information The protein is represented with a multiple sequence alignment and the ligand as a SMILES string, allowing for unconstrained flexibility in the protein-ligand interface. There are two versions of Umol: one that uses protein pocket...
Edgar RC., Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny.Nature Communications13.1 (2022): 6968. https://www.nature.com/articles/s41467-022-34630-w.pdf Edgar RC. and Tolstoy I., Muscle-3D: scalable multiple protein structure alignment (...