VMD is a visualization program developed by the Resource and designed for interactive display and analysis of biomolecular systems [13]. The program is capable of animation, manipulation and analysis of proteins, nucleic acids, lipid membranes and other biological molecules. It supports OpenGL and SGI GL graphics libraries with stereo displays. Moreover, VMD supports output formats for VRML (Virtual Reality Modeling Language) and many popular renderers (RayShade, POV-Ray and Raster3D). VMD can read many different file formats directly and through an interface with the program Babel [58]. The wide variety of methods for rendering and coloring molecules offered by VMD includes VdW, licorice, cartoon and surface models. Animation information can come from a trajectory file or by connecting to a running simulation program, such as NAMD [19, 59]. The VMD scripting language is based on TCL/TK. It may be used to query molecular information, perform analysis and display the res ults interactively, yielding a powerful base for implementing new methods in structure visualization and analysis. To further method development, the complete C++ source code is freely available to the biomedical community, along with documentation for using and modifying the program. Version 1.2 of VMD runs under most versions of Unix, including IRIX, Linux and Solaris, and will soon be ported to Windows NT. See the VMD home page for more information.*

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
3P41RR005969-09S1
Application #
6295235
Study Section
Project Start
1999-02-01
Project End
1999-07-31
Budget Start
1997-10-01
Budget End
1998-09-30
Support Year
9
Fiscal Year
1999
Total Cost
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
Radak, Brian K; Chipot, Christophe; Suh, Donghyuk et al. (2017) Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 13:5933-5944
Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V et al. (2016) Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry 55:5714-5725
Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
Poudel, Kumud R; Dong, Yongming; Yu, Hang et al. (2016) A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 27:2119-32
Vermaas, Josh V; Taguchi, Alexander T; Dikanov, Sergei A et al. (2015) Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Biochemistry 54:2104-16
Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P et al. (2015) Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 9:10598-611
Shen, Rong; Han, Wei; Fiorin, Giacomo et al. (2015) Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 11:e1004368

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