The performance of ACCLUSTER was also compared with PepSite2 and PeptiMap, two recently developed methods developed for identifying peptide binding sites. The results showed that ACCLUSTER is a promising method for peptide binding site prediction. Additionally, ACCLUSTER was also shown to be ...
Parallel models for structure and sequence-based peptide binding site prediction Fig. 1: Model architecture and training procedure. Full size image Transfer learning results in large improvements in model performance Fig. 2: Impact of transfer learning on model performance on the peptide complex validat...
PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res. 2012;40:W423-7... Ryan E. Odstrcil Ryan E. OdstrcilSchool of Mechanical and Materials Engineering, Washington State University, Pullman ,Washington , United StatesMore by Ryan E. Odstrcil,RE Odstrcil,More ...
It is worth noting that molecular docking can be used with two distinct objectives: (i) structure-based binding affinity estimation, or (ii) geometry prediction (also referred to as geometry optimization)14,27. For instance, recent publications use molecular docking or other structural analyses as ...
MHCflurry implements class I peptide/MHC binding affinity prediction. The current version provides pan-MHC I predictors supporting any MHC allele of known sequence. MHCflurry runs on Python 3.9+ using thetensorflowneural network library. It exposescommand-lineandPython libraryinterfaces. ...
Prediction of a receptor–peptide complex involves two layers of complexity: prediction of (i) the peptide's binding site on the receptor and (ii) the structure of the bound peptide on the receptor (Peterson et al., 2017). As addressing both problems is a challenging task, the majority of...
Then, computationalprediction of the peptide- binding sites isdesirable. Popular programs for protein-peptide docking usually depend stronglyon the initial positions of peptides, such as Rosetta. To overcome thislimitation, here we develop a global docking approach in which the peptide isinitially ...
The predictive ability of these QMs was tested using an external test set and compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0, showing significantly improved predictions for three of the four DP proteins, when ...
and more than 70% of all sequences can be partially modeled from known structures with homologous domains.8This has been reflected in the human genome sequence.9Impressive progress has already been made in computational protein prediction and design, principally based on the known structural elements...
Ngo JT, Marks J, Karplus M, “Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox,” The Protein Folding Problem and Tertiary Structure Prediction, K. Merc Jr. and S. Le Grand Edition, 1994, pp. 491-495. ...