Related Experiment Video
Updated: Jul 2, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
CHARMMing: a new, flexible web portal for CHARMM
Benjamin T Miller1, Rishi P Singh, Jeffery B Klauda
1Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Journal of Chemical Information and Modeling
|August 14, 2008
Summary
CHARMMing offers a user-friendly web portal for molecular simulations, simplifying preparation, submission, and visualization. This tool, including GENRTF and a job broker, aids newcomers in molecular modeling with proteins like 1YJP.
Area of Science:
- Computational Chemistry
- Structural Biology
- Bioinformatics
Background:
- Molecular modeling is crucial for understanding biological systems.
- Existing tools for molecular simulations can have steep learning curves.
- CHARMM is a widely used package for macromolecular modeling.
Purpose of the Study:
- To introduce CHARMMing, a new web portal for the CHARMM package.
- To provide a user-friendly interface for molecular simulations.
- To facilitate the use of grid and cluster computing for CHARMM simulations.
Main Methods:
- Development of a web portal (CHARMMing) with an integrated graphical user interface.
- Integration of GENRTF for defining non-standard force field features.
- Implementation of a job broker for portable grid and cluster computing.
- Demonstration of CHARMMing with protein simulations (1YJP, 1O1O, 1UFY).
Main Results:
- CHARMMing provides a streamlined workflow for molecular simulation preparation, submission, monitoring, and visualization.
- GENRTF extends CHARMM's force field capabilities.
- The job broker enables efficient use of distributed computing resources.
- The portal simplifies the introduction of new users to molecular modeling.
Conclusions:
- CHARMMing enhances accessibility to molecular modeling simulations.
- The integrated tools and user-friendly interface lower the barrier for researchers.
- CHARMMing supports advanced computational approaches like grid and cluster computing.
Related Concept Videos
03:00Molecular Chaperones and Protein Folding
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
The...
03:00Molecular Chaperones and Protein Folding
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
The...
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
02:30Chirality at Nitrogen, Phosphorus, and Sulfur
Chirality is most prevalent in carbon-based tetrahedral compounds, but this important facet of molecular symmetry extends to sp3-hybridized nitrogen, phosphorus and sulfur centers, including trivalent molecules with lone pairs. Here, the lone pair behaves as a functional group in addition to the other three substituents to form an analogous tetrahedral center that can be chiral.
A consequence of chirality is the need for enantiomeric resolution. While this is theoretically possible for all...
A consequence of chirality is the need for enantiomeric resolution. While this is theoretically possible for all...
02:25Chirality
Chirality is a term that describes the lack of mirror symmetry in an object. In other words, chiral objects cannot be superposed on their mirror images. For example, our feet are chiral, as the mirror image of the left foot, the right foot, cannot be superposed on the left foot.
Chiral objects exhibit a sense of handedness when they interact with another chiral object. For example, our left foot can only fit in the left shoe and not in the right shoe. Achiral objects — objects that have...
Chiral objects exhibit a sense of handedness when they interact with another chiral object. For example, our left foot can only fit in the left shoe and not in the right shoe. Achiral objects — objects that have...