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- TINKER
A complete package for molecular mechanics, dynamics and modeling of
molecules, especially biomacromolecules. TINKER has the ability to use
any of several common parameter sets, such as Amber (ff94, ff96, ff98,
ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS
(OPLS-UA, OPLS-AA and OPLS-AA/L), as well as our own AMOEBA polarizable
atomic multipole force field. TINKER implements a variety of novel
algorithms including distance geometry with fast metrization and
Gaussian trial distances, Elber's reaction path method, global
optimization via our Potential Smoothing and Search algorithms,
molecular dynamics with simulated annealing and stochastic dynamics
options, particle mesh Ewald summation, Monte Carlo minimization,
atomic multipole treatment of electrostatics with explicit dipole
polarizability, Eisenberg-McLachlan ASP and GB/SA continuum solvation
models, and truncated Newton TNCG local energy minimization.
- FORCE FIELD EXPLORER
A Java-based molecular modeling program that serves as a graphical
user interface (GUI) to the TINKER program package. Systems can be
visualized using common representations such as wireframe, ball & stick,
tubes and spacefilled models. Beyond visualization techniques, Force
Field Explorer provides a graphical user interface for editing keyword
files that control TINKER execution, launching analysis, optimization,
molecular dynamics, etc. jobs, and viewing the results. The
current version runs on Windows, Macintosh and Linux systems.
- SLEUTH
A small set of programs that allow creation of PDB file summaries and
searching of a dataset extracted from the PDB for structural motifs. For
example, SLEUTH can find all examples of type I turns that match some
generalized sequence pattern. An additional program implements the
Eisenberg 3D profile algorithm. The /data subdirectory contains a set of
summary files with dihedral angle values, secondary structure and solvent
exposure data by residue for many of the current PDB structures.
- PROPAK
A program to attack the "inverse" protein folding problem
via modeling of the side chain packing in proteins. Allows the user to
redesign a portion of a known structure using a library of side chain
rotamers. Provides a list of the amino acid sequences that are predicted
be compatable with an input tertiary fold. The PROPAK algorithm was one
of the first attempts to attack this general protein design problem.
The original program, although still useful, has not been under active
development for some time and is largely superceded by methods from
the labs of Steve Mayo, David Baker, and many others.
- QSAR
A program to derive QSAR models via regression analysis. The analysis
can be performed by ordinary least squares (OLS), principal components
(PCR) or partial least squares (PLS). "Leave-1-out"
cross-validation is performed for all three types of analysis. For OLS
and PCR, variable selection can be performed via simulated annealing on
predictive power. In all cases, the final QSAR model can be used to make
predictions for a test set distinct from the training set. Several training
set data tables, including Garland Marshall's VALIDATE set for prediction
of binding in macromolecular complexes, are provided as examples.
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