Dockground: A comprehensive data resource for modeling of protein complexes
Sign Up to like & getrecommendations! Published in 2018 at "Protein Science"
DOI: 10.1002/pro.3295
Abstract: Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein–protein complexes accounts only for a fraction of known protein interactions. This gap in… read more here.
Keywords: protein; modeling protein; protein interactions; resource ... See more keywords
Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8736-8_17
Abstract: Proteins are subject to evolutionary forces that shape their three-dimensional structure to meet specific functional demands. The knowledge of the structure of a protein is therefore instrumental to gain information about the molecular basis of… read more here.
Keywords: three dimensional; modeling protein; information; biology ... See more keywords
Homology Modeling of Protein Targets with MODELLER.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9752-7_15
Abstract: Homology modeling is a computational approach to generate three-dimensional structures of protein targets when experimental data about similar proteins are available. Although experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy successfully solved… read more here.
Keywords: modeling protein; targets modeller; homology modeling; spectroscopy ... See more keywords
Modeling protein-protein interactions through alanine-amide hydrogen bonds
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DOI: 10.1007/s11224-018-1127-z
Abstract: The hydrogen-bonded complexes formed between alanine and formamide and between alanine and N-methylformamide have been completely investigated in the present study using ab initio molecular orbital theory (MP2) and density functional theory (B3LYP) using aug-cc-pVDZ… read more here.
Keywords: protein; modeling protein; interactions alanine; protein interactions ... See more keywords
Computational modeling of protein assemblies.
Sign Up to like & getrecommendations! Published in 2017 at "Current opinion in structural biology"
DOI: 10.1016/j.sbi.2017.04.006
Abstract: Computational methods to predict the 3D structures of protein interactions fall into 3 categories-template based modeling, protein-protein docking and hybrid/integrative modeling. The two most important considerations for modeling methods are sampling and scoring conformations. Sampling… read more here.
Keywords: protein; modeling protein; microscopy; computational modeling ... See more keywords
Modeling Protein-Based Hydrogels under Force.
Sign Up to like & getrecommendations! Published in 2018 at "Physical review letters"
DOI: 10.1103/physrevlett.121.168101
Abstract: Hydrogels made from structured polyprotein domains combine the properties of cross-linked polymers with the unfolding phase transition. The use of protein hydrogels as an ensemble approach to study the physics of domain unfolding is limited… read more here.
Keywords: protein; based hydrogels; modeling protein; protein based ... See more keywords
Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints
Sign Up to like & getrecommendations! Published in 2021 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1009107
Abstract: We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a… read more here.
Keywords: deer; methodology; modeling protein; protein conformational ... See more keywords