Search engine for discovering works of Art, research articles, and books related to Art and Culture
Javascript must be enabled to continue!
NMR Refinement and Peptide Folding Using the GROMACS Software
View through CrossRef
Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.
Title: NMR Refinement and Peptide Folding Using the GROMACS Software
Description:
Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins.
Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations.
Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software.
With this package it is possible to model distance restraints, dihedral restraints and orientation restraints.
The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.
Related Results
Cotranslational protein folding can promote the formation of correct folding intermediate
Cotranslational protein folding can promote the formation of correct folding intermediate
Abstract
Cotranslational folding is vital for proteins to form correct structures in vivo. However, it is still unclear how a nascent chain folds at atomic resoluti...
Learnings from a New Slim Hole LWD NMR Technology
Learnings from a New Slim Hole LWD NMR Technology
Abstract
This paper presents recent experience with a new 4 ¾-in logging-while-drilling (LWD) nuclear magnetic resonance (NMR) tool. Data from several wells drilled ...
Key Insights from Comparing LWD and Core NMR in Heavy Oil Carbonates
Key Insights from Comparing LWD and Core NMR in Heavy Oil Carbonates
Abstract
Recent advances in LWD (logging-while-drilling) NMR (nuclear magnetic resonance) have enabled the simultaneous measurement of T1 and T2. These advances b...
Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids
Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids
Isolation, characterization of natural products dimeric amide alkaloids from roots of the Piper chaba Hunter. The synthesis of these products using intermolecular [4+2] cycloaddit...
Anemia Is Inversely Associated with Serum C-Peptide Concentrations in Patients with Type 2 Diabetes
Anemia Is Inversely Associated with Serum C-Peptide Concentrations in Patients with Type 2 Diabetes
Results: The aim of the study was to investigate the relationship between anemia and serum C-peptide concentrations in Korean patients with type 2 diabetes. A total of 1,300 subjec...
Accurate Rock Mineral Characterization With Nuclear Magnetic Resonance
Accurate Rock Mineral Characterization With Nuclear Magnetic Resonance
Nuclear magnetic resonance (NMR) logging is a powerful formation evaluation technology that provides mineralogy-independent porosity and helps distinguish clay-bound water, capilla...
The Role of NMR Spectroscopy in Understanding How Proteins Fold
The Role of NMR Spectroscopy in Understanding How Proteins Fold
Proteins are synthesized within the cell on ribosomes. Although there is debate as to the beginnings of folding, it is clear that the major events in the folding process of a prote...
In vivo aspects of protein folding and quality control
In vivo aspects of protein folding and quality control
BACKGROUND
Proteins are synthesized on ribosomes as linear chains of amino acids and must fold into unique three-dimensional structures to fulfill their biologi...