… of protein models. Nevertheless, it is instructive to make a historical analysis of some of the
early modeling studies based on knowledge of homologous or other proteins with a common …

… to build protein models from structural … protein modeling can be identified and used for
model building. Furthermore, we will report on two recent examples of knowledge-based model …

… Protein Data Bank (PDB)," the number of protein sequences in the Swiss-Protº database is
more than 40,000. Knowledge-based modeling works … For protein cores sharing 50% residue …

… is knowledge-based, depending on the structures of homologous or analogous proteins and
more … However, these models have been limited by errors inherent in structures defined by …

… design by improving the accuracy of physics-based models of … Recently, knowledge-based
potentials (in isolation or in … of existing protein function, the redesign of natural protein folds …

… Since knowledge-based methods are less compute … suitable knowledge-based tools for
modeling protein–peptide complexes would permit quick structural analysis of MHCs and protein …

… use of knowledge-based potentials for the analysis of protein interactions. In Section 2, we
introduce knowledge-based potentials … 3 Modeling of Protein Interactions Using Templates, 4 …

… Computational tools can be used to model the structure of peptides targeting protein … - and
knowledge-based approach to model the conformation of peptides targeting protein interfaces…

… , into an averaged binding-site representation of the generated binding-site models (step
2), we generate new protein models, now considering explicitly the docked ligand(s) (step 3a). …

… knowledge-based statistical potentials, which derive energy functions from statistical analysis
of known structures of proteins or protein−ligand (or protein−protein) … than the modeling of …