There exist many tools for computing both sequence-based and structure-based features for proteins. Previous research by Jones and Thornton [55] into identifying important features for PPI site prediction has revealed solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion, ...
& Holm, L. PANNZER—a practical tool for protein function prediction. Protein Sci. 31, 118–128 (2022). Article PubMed Google Scholar Kulmanov, M., Zhapa-Camacho, F. & Hoehndorf, R. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Res....
amino acid composition and functional motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction.To predict the subcellular localization of your target protein, simply paste your protein's amino acid sequence (single letter code) in the WoLF PSORT window below and click...
A Deep Learning based protein flexibility prediction tool. Abstract Information on the protein flexibility is essential to understand crucial molecular mechanisms such as protein stability, interactions with other molecules and protein functions in general. B-factor obtained in the X-ray crystallography exp...
proteins with similar sequences can have a different set of functions depending on their active sites and the organisms in which they are a part. Consequently, methods that use the same sources of information for all three subontologies of GO are limited; while functions from the MFO subontolog...
AUGUSTUS consists of augustus, the gene prediction tool, additional C++ tools located in Augustus/auxprogs and Perl scripts located in Augustus/scripts. Perl scripts must be executable (see instructions in section BRAKER components. The C++ tool bam2hints is an essential component of BRAKER when ru...
2D structure prediction tools NNcon and SVMcon for general residue-residue contact prediction Residue-residue contact prediction continues to be an area of active research and becoming of greater importance in the latest rounds of CASP. Of particular importance to tertiary structure prediction are sequ...
The structure-based virtual screening of flavonoids indicated that most flavonoids can bind to the acetylated lysine (KAc) binding site of BD1 of Brd4 receptor molecule and can act as novel natural bromodomain inhibitors. Flavonoids were found to occupy the active site, forming hydrogen bonds between...
Our computational prediction is based on a physics-based scoring function and Monte Carlo movements to accurately simulate the protein diffusion and conformational changes. This CG model therefore attempts to mimic the biological process of protein association ab initio. It has been proposed that the ...
The accuracy of SCUBA-D, a protein backbone structure diffusion model trained independently and orthogonally to existing protein structure prediction networks, is confirmed by the X-ray structures of 16 designed proteins and a protein complex, and by experimental validation of designed heme-binding prot...