|
Software |
|
AMBER Molecular
Simulation Package |
A package of molecular simulation
programs. The current version of the code is Amber version 9, which
is distributed by UCSF. |
|
Gaussian |
A connected system of programs for
performing semi-empirical and ab initio molecular orbital (MO)
quantum chemical calculations. |
|
GNUPlot |
A free, command-driven, interactive,
function and data plotting program. |
|
VMD |
A molecular visualization program for
displaying, animating, and analyzing large biomolecular systems
using 3-D graphics and built-in scripting. |
|
OpenBabel |
A chemical toolbox designed to search,
convert, analyze, or store data from molecular modeling, chemistry,
biochemistry, or related areas. |
|
JOE |
My favorite text editor, which is
capable of emulating WordStar, Pico, and Emacs. |
|
SUSE Linux |
Suse Linux Operating System |
|
3DNA |
A package for the analysis, rebuilding,
and visualization of 3D nucleic acid structures. |
|
SPARKY |
A graphical NMR assignment and
integration program for proteins, nucleic acids, and other polymers. |
|
NMRPipe Spectral
Processing and
Analysis System |
A program for Fourier processing of
spectra in one to four dimensions, as well as a variety of
facilities for spectral display and analysis. |
|
Delphi |
A program that provides numerical
solutions to the Poisson-Boltzmann equation (both linear and
nonlinear form) for molecules of arbitrary shape and charge
distribution. |
|
GRASP |
A molecular visualization and analysis
program, which is particularly useful for the display and
manipulation of the surfaces of molecules and their electrostatic
properties. |
|
GAMESS |
The General Atomic and Molecular
Electronic Structure System (GAMESS) is a general ab initio quantum
chemistry package. |
|
GROMACS |
A package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles. |
|
GRACE |
A 2D plotting tool for the X Window
System and M*tif. |
|
GROMOS |
A general-purpose molecular dynamics
computer simulation package for the study of biomolecular systems. |
|
Journals |
|
|
|
Structural Database |
AMBER Force Field Database |
|
The Nucleic Acid
Database (NDB) |
AMBER
Parameter Database |
|
The Protein Data Bank (PDB) |
RNA Modified Parameters Database |
|
The RNA Structure
Database |
|
|
Structural
Classification of RNA |
|
|
National Center for
Biotechnology Information |
|
|
Nucleic Acid Interaction
Library |
|
|
Macromolecular Structure
Database (MSD) |
|
|
Other Links |
|
ISI Web of Knowledge |
An integrated Web-based platform
providing high-quality content and tools to access, analyze, and
manage research information, such as cross-product searching, links
to full text, citation alerts, table of contents alerts, personal
journal lists, and personal bibliographic management. |
|
Turner Group |
Prof. Douglas H. Turner's Research Group
University of Rochester, Department of
Chemistry, Rochester, NY |
|
The RNA World (3rd Ed.) |
Read the chapters of 'The RNA World, 3rd
Ed.' online for free. |
|
TERAGRID |
An open scientific discovery
infrastructure combining leadership class resources at nine partner
sites to create an integrated, persistent computational resource. |
|
Running Jobs on NCSA (info) |
How to run Jobs on NCSA's Xeon Linux
Cluster (one of the sites of Teragrid server): running mpi programs,
queues, LSF batch commands, sample batch scripts. |
