VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program
نویسندگان
چکیده
UNLABELLED Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs. One of the beneficial properties of the VMD is its ability to be extendable by designing new plug-in. We introduce here a new facility of the VMD for distance analysis and radius of gyration of biopolymers such as protein and DNA. AVAILABILITY The database is available for free at http://trc.ajums.ac.ir/HomePage.aspx/?TabID/=12618/&Site/=trc.ajums.ac/&Lang/=fa-IR.
منابع مشابه
Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...
متن کاملEnergy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...
متن کاملPreliminary Evaluation for Vacuum Membrane Distillation (VMD) Energy Requirement
The energy requirement of vacuum membrane distillation (VMD) with or without recirculation was modelled using both experimental results and theoretical data. The trends are generally consistent between the theoretical and experimental data. Thermal energy contributes the most to the total energy required for the VMD process. To lower the thermal energy cost, waste heat resource and heat recover...
متن کاملJust How Strange? Loops, Poles and the Strangeness Radius of the Nucleon
We consider a simple model for the strangeness radius of the nucleon. The model is based on vector meson dominance (VMD) and ω − φ mixing in addition to a kaon cloud contribution. We find that the VMD contribution is similar in magnitude and of the same sign as the kaon contribution to the Sachs strangeness radius and is significantly larger than the kaon contribution to the Dirac radius.
متن کاملUsing Tcl for molecular visualization and analysis.
Reading and manipulating molecular structure data is a standard task in every molecular visualization and analysis program, but is rarely available in a form readily accessible to the user. Instead, the development of new methods for analysis, display, and interaction is often achieved by writing a new program, rather than building on pre-existing software. We present the Tcl-based script langu...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 8 شماره
صفحات -
تاریخ انتشار 2012