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
Sign Up to like & getrecommendations! Published in 2018 at "Structural Chemistry"
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-ligand interactions for drug discovery in the era of deep learning.
Sign Up to like & getrecommendations! Published in 2025 at "Chemical Society reviews"
DOI: 10.1039/d5cs00415b
Abstract: Accurate modeling of protein-ligand interactions is a cornerstone of rational drug discovery, yet persistent challenges remain due to the intricate complexity of molecular interactions and the limitations of conventional physics-based computational methods. Approaches such as… read more here.
Keywords: drug discovery; drug; protein ligand; modeling protein ... See more keywords
Integrated modeling of protein and RNA
Sign Up to like & getrecommendations! Published in 2024 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbae139
Abstract: Haoquan Liu is a PhD student in the College of Physical Science and Technology at Central China Normal University. His research is centered around network science and deep learning, particularly in the field of biomolecule… read more here.
Keywords: integrated modeling; protein rna; modeling protein;
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