Proteus and the design of ligand binding sites
dc.contributor.author | Polydorides, Savvas | en |
dc.contributor.author | Michael, E. | en |
dc.contributor.author | Mignon, D. | en |
dc.contributor.author | Druart, Karen | en |
dc.contributor.author | Archontis, Georgios Z. | en |
dc.contributor.author | Simonson, T. | en |
dc.creator | Polydorides, Savvas | en |
dc.creator | Michael, E. | en |
dc.creator | Mignon, D. | en |
dc.creator | Druart, Karen | en |
dc.creator | Archontis, Georgios Z. | en |
dc.creator | Simonson, T. | en |
dc.date.accessioned | 2019-12-02T15:32:28Z | |
dc.date.available | 2019-12-02T15:32:28Z | |
dc.date.issued | 2016 | |
dc.identifier.issn | 1064-3745 | |
dc.identifier.uri | http://gnosis.library.ucy.ac.cy/handle/7/59011 | |
dc.description.abstract | This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding affinities. The software offers the use of several molecular mechanics force fields and solvent models, including two generalized Born variants, and a large range of scoring functions, which can combine protein stability, ligand affinity, and ligand specificity terms, for positive and negative design. We present in detail the steps for structure preparation, system setup, construction of the interaction energy matrix, protein sequence and structure optimizations, pKα calculations, and ligand titration calculations. We discuss illustrative examples, including the chemical/structural optimization of a complex between the MHC class II protein HLA-DQ8 and the vinculin epitope, and the chemical optimization of the compstatin analog Ac-Val4Trp/His9Ala, which regulates the function of protein C3 of the complement system. © Springer Science+Business Media New York 2016. | en |
dc.source | Methods in Molecular Biology | en |
dc.source.uri | https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964310685&doi=10.1007%2f978-1-4939-3569-7_6&partnerID=40&md5=4bff5dcf41f0511a21b184842fdda61e | |
dc.subject | amino acid sequence | en |
dc.subject | protein | en |
dc.subject | binding affinity | en |
dc.subject | complement component C3 | en |
dc.subject | major histocompatibility antigen class 2 | en |
dc.subject | chemistry | en |
dc.subject | molecular mechanics | en |
dc.subject | thermodynamics | en |
dc.subject | calculation | en |
dc.subject | Ligands | en |
dc.subject | ligand | en |
dc.subject | protein conformation | en |
dc.subject | Proteins | en |
dc.subject | vinculin | en |
dc.subject | protein stability | en |
dc.subject | binding site | en |
dc.subject | Binding Sites | en |
dc.subject | epitope | en |
dc.subject | alanine | en |
dc.subject | ligand binding | en |
dc.subject | histidine | en |
dc.subject | pKa | en |
dc.subject | valine | en |
dc.subject | Protein design | en |
dc.subject | Generalized Born model | en |
dc.subject | HLA DQ8 antigen | en |
dc.subject | Implicit solvent | en |
dc.subject | Ligand design | en |
dc.subject | Monte Carlo | en |
dc.subject | software design | en |
dc.title | Proteus and the design of ligand binding sites | en |
dc.type | info:eu-repo/semantics/article | |
dc.identifier.doi | 10.1007/978-1-4939-3569-7_6 | |
dc.description.volume | 1414 | |
dc.description.startingpage | 77 | |
dc.description.endingpage | 97 | |
dc.author.faculty | Σχολή Θετικών και Εφαρμοσμένων Επιστημών / Faculty of Pure and Applied Sciences | |
dc.author.department | Τμήμα Φυσικής / Department of Physics | |
dc.type.uhtype | Article | en |
dc.description.notes | <p>Cited By :1</p> | en |
dc.source.abbreviation | Methods Mol. Biol. | en |
dc.contributor.orcid | Archontis, Georgios Z. [0000-0002-7750-8641] | |
dc.gnosis.orcid | 0000-0002-7750-8641 |
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