Molecular-dynamics Simulations of Biological Systems
AbstractOne of the main tools for studying biological molecules is the method of computer modelling based on molecular dynamics (MD). MD simulations provide detailed information about the fluctuations and conformational changes of proteins and nucleic acids. This method is routinely used for investigations of the structure, dynamics and thermodynamics of biological molecules and their complexes. In the literature, results of MD simulation of proteins dissolved in water, protein--DNA complexes and lipid systems, dealing with various aspects of the thermodynamics of ligand binding and folding and packaging of relatively small (short) proteins are continually published. Nowadays, there are many specialized techniques for solving particular problems, including those listed above, which take into account quantum-mechanical effects as well. The MD modelling technique is also widely used for determining the spatial structure of biological molecules by analyzing the information obtained by means of X-ray diffraction and nuclear magnetic resonance. ...
The journal Biomath Communications is an open access journal. All published articles are immeditely available online and the respective DOI link activated. All articles can be access for free and no reader registration of any sort is required. No fees are charged to authors for article submission or processing. Online publications are funded through volunteer work, donations and grants.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License 4.0 that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).