PEST
- Public EPR Software Tools. This software is provided
free to the
EPR research community with the understanding that any resulting
report either internally or externally distributed explicitly
acknowledge this contribution.
PHYLIP
- the PHYLogeny Inference Package is a package of
programs for
inferring phylogenies (evolutionary trees). [added 12/30/2000]
PIMM
- a Pi-SCF-Molecular Mechanics Program. Contact Prof.
Lindner [modified 1/1/2001]
PLATON
- a versatile SHELX97 compatible multipurpose
crystallographic tool. Most PLATON features complement those available in the
excellent and widely distributed 'public domain' SHELX97 package for crystal
structure determination and refinement. [added 1/13/2001]
PASTA
- Protein ASsignment by Threshold Accepting. [added
1/18/2001]
POLYRATE
- is a computer program for the calculation of chemical
reaction rates of polyatomic species (and also atoms and diatoms as special
cases). [modified 1/18/2001]
PovChem
- a chemical visualization and illustration program
with a new graphic interface. It takes molecules in the PDB format, lets you
to set up a picture with fine control over details of the illustration -
colors, atom and bond radii, view orientation, etc. It will even calculate and
display hydrogen bonds. It then exports the picture in POV-Ray format, which
allows you to render the image with a state-of-the-art raytracer, giving
high-quality images at any resolution, for anything from web page thumbnails
to full-size high-resolution images. [added 1/13/2001]
PQS
- an ab-initio module capabilities: RHF and UHF SCF and
DFT energies and gradients, including several initial wavefunction guess
options; all popular exchange-correlation functionals; efficient, flexible
geometry optimization for all these methods including Baker's Eigenvector
Following (EF) algorithm for minimization and saddle-point search, Pulay's
GDIIS algorithm for minimization, use of Cartesian, Z-matrix and delocalized
intenal coordinates; all ab initio modules except MP2 and NBO are fully
parallel. [modified 1/18/2001]
PROCHECK
- checks the stereochemical quality of a protein
structure, producing a
number of PostScript plots analysing its overall and
residue-by-residue geometry. The plots can be also in he plots can be
also in colour.
Pronto
- The Protein 3D NMR Tool. [added 1/18/2001]
Prospect
- PROtein Structure Prediction and Evaluation Computer
Toolkit is a
threading-based protein structure prediction system. PROSPECT is
designed particularly for the recognization of the fold template
whose sequence has insignificant homology to the target
sequence.
PyMOL
- is a molecular graphics program which uses Python as
its scripting
language. It is still under development and is not yet ready for
usage by novices. However, experienced molecular graphics users and
developers who know Python may find it valuable in its present
form.
Q-Chem
- is a modern ab initio quantum chemistry software
package capable of
analyzing large structures in practical amounts of time without
compromising accuracy.
QikProp
- provides rapid predictions for physically-significant
descriptors and
pharmaceutically-relevant properties of neutral organic molecules.
Accurate predictions are made for free energies of solvation in
hexadecane, octanol, and water, octanol/water partition coefficient
(log P), aqueous solubility (log S), and Caco-2 cell permeabilty.
Results for libraries of compounds are output in a format ready for
facile incorporation into spreadsheet and QSAR programs.
QMol
- is a program for viewing molecular structures and
animating molecular
trajectories. It supports: display wire frame and space-filling
molecular structures from a PDB file; animate molecular trajectories
stored in the DCD file format; interactively measure bond lengths,
bond angles and torsion angles; dynamically adjust user selected
torsion angles; display atom labels.
QSite
- is a new mixed mode QM/MM program for highly accurate
energy
calculations of protein-ligand interactions in the active site. The
program is specifically designed for proteins and allows a number of
different QM/MM boundaries for residues in the active site. QSite
uses the power and speed of Jaguar to perform the QM part of the
calculations and OPLS-AA to perform the MM part perform the MM part
of the calculations.
RasMol
- molecular graphics program intended for the
visualisation of
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images. The
RPM packages can be also found at Kin
Taishin@JAIST website. [modified 1/18/2001]
Raster3D
- set of tools for generating high quality raster
images of
proteins or other molecules. The core program renders spheres,
triangles, cylinders, and quadric surfaces with specular
highlighting, Phong shading, and shadowing. It uses an efficient
software Z-buffer algorithm which
is independent of any graphics hardware. Ancillary programs process
atomic coordinates from Brookhaven PDB files into rendering
descriptions for pictures composed of ribbons, space-filling atoms,
bonds, ball+stick, etc. Raster3D can also be used to render pictures
composed in other programs. The RPM packages can be also found at Kin
Taishin@JAIST website.
Ribbons
- designed to display molecular models as rendered
images. The data necessary consist of atomic
coordinates in Protein Databank format and files of color-coding information.
[added 1/13/2001]
RdLength
- calculates the Radiation Length of a single molecule
based on its
empirical formula. The unit used is g/cm2.
Remos
- is a structure determination program for modulated
structures. [added
1/3/2001]
RnaViz
- is a user-friendly, portable, windows-type program
for producing
publication-quality secondary structure drawings of RNA molecules.
Drawings can be created starting from DCSE alignment files if they
incorporate structure information or from mfold ct files. The layout
of a structure can be changed easily. Display of special structural
elements such as pseudo-knots or unformatted areas is possible.
Sequences can be automatically numbered, and several other types of
labels can be used to annotate particular bases or areas.
SDS'94
- a computing system for solving and refinement of
monocrystallic
ordinary crystal structures. It consists of several independent
programs which do all the work from data reduction to the refinement
and distances calculation. [added 1/5/2001]
SgInfo
- a comprehensive Collection of ANSI C Routines for
the Handling of
Space Group Symmetry. [added 1/5/2001]
Sharp
- a computer program for macromolecular
crystallography. It operates on reduced, merged and scaled data from SIR(AS),
MIR(AS) and MAD experiments, refines the heavy-atom model, helps detect minor
or disordered sites using likelihood-based residual maps, and
calculates phase probability distributions for all reflexions in the dataset.
[added 1/18/2001]
SCHAKAL
- a FORTRAN program for the graphical
representation of molecular and solid-state models. [added 1/18/2001]
SHELL
- is a free energy calculation and minimisation program
for crystals
which uses lattice statics and quasiharmonic lattice dynamics to calculate the
free energy and its derivatives with respect to geometrical parameters.
Because the calculations are all analytic, this can give very fast and precise
results for optimal crystal geometry at finite temperatures and pressures.
[added 1/8/2001]
SHELX
- is a set of programs for crystal structure
determination from
single-crystal diffraction data. [added 1/5/2001]
SHELX-to-ORTEP
- converter module. [added 1/13/2001]
SIgMA
- SImulations of MAcromolecules is a system of programs
and data
files for doing: energy minimization, free MD, constrained and
restrained MD, MD with free-energy methods of biological
macromolecules. Using SIgMA one can work with periodic boundary
conditions and simulate molecules in solvent water. (In principle,
SIgMA can also handle the more complex periodicity of crystals.
However, the currently running fast version of SIgMA cannot handle
any except orthogonal P1 "symmetry".
Simbiosys Inc. products
- The product line of Simbiosys consists of a series of
highly focused and specialised client application tools
targeting various stages and techniques of molecular modelling in biochemical
systems with special attention to the drug discovery process utilised by the
pharmaceutical industry. All of these client applications utilise the MoDeST
(Molecular Design Software Toolkit) server and the CheVi (Chemical Visualizer)
library. Simbiosys also distributes: SPROUT - de novo ligand
design software, and CLiDE - Chemical
Literature Data Extraction software. [added 1/18/2001]
SIMPRO
- a Program for Structure determination, Diffraction,
Materials Science,
Chemistry. Full Powder Pattern Fitting Program. Refinement of
multiple phases, of the wave vector components of a modulated
structures, Lorentz polarisation. [added 1/5/2001]
SIMPSON
- is a General Simulation Program for Solid-State NMR.
It features
multi-pulse 1D/2D experiments on large spin-systems with input-files
implemented using a simple scripting language. The program is
designed to emulate a NMR spectrometer by letting the user specify
high-level NMR concepts such as spin systems, nuclear spin
interactions, rf irradiation, free precession, phase cycling,
coherence-order filtering, and implicit/explicit acquisition.
SIMREF
-
Structure determination, Diffraction, Materials Science, Chemistry.
Simultaneous Rietveld Refinement with Multiple Powder Data sets. [added
1/5/2001]
Sir92
- a program for automatic solution of crystal
structures by direct
methods. The method for the automatic structure determination is
based on the representation theory. 1-phase structure seminvariants
and 3-phase structure invariants are estimated via their second
representation, 2-phase seminvariants and 4-phase invariants via
their first representation. SIR92 is the heir of SIR88 of which it retains
most of the features.
Situs
- A program package for the docking of protein crystal
structures to single-molecule, low-resolution maps from
electron microscopy or small angle X-ray scattering. [added 1/20/2001]
SnB
- a program based on Shake-and-Bake, a dual-space
direct-methods procedure for determining crystal structures from X-ray
diffraction data. [added 1/18/2001]
SOLVATE
- is a program to construct an atomic solvent
environment model for a
given atomic macromolecule model (solute) for use in MD simulations.
It generates irregularly-shaped solvent volumes, adapted to a given
solute's structure; allows efficient computation of boundary forces
as required in MD simulations; guarantees a minimal
solute-boundary-distance; allows to specify a minimum solvent surface
curvature in order to avoid `flat' surface regions; generates
`disordered' (= fluid) water, not a (= fluid) water, not a grid of
water molecules (= ice); locally minimizes the positions of all water
molecules; optionally places salt ions () obeying a Debye-Hückel
distribution; optionally places (and marks) buried water molecules;
and is X-PLOR/CHARMm-compatible, i.e., input and
output is in pdb-/psf-format.
Sparkle
Metals
- Lanthanide/Rare-Earth/Metal MOPAC calculations. Now
Possible! An
essentially electrostatic lanthanide-ligand bonding description.
Given the large degree of ionic bonding in lanthanides, this method
works very well when used in the appropriate circumstances. The
method is simple, but ingenious. [added 12/30/2000]
Sparky
- a graphical NMR assignment and integration program
for proteins, nucleic acids, and other polymers. [added 1/18/2001]
Spin
- SPIN NMR simulation program. [added 1/18/2001]
Spock
- is a full-featured molecular graphics program. Spock
has been
designed from the ground up to be powerful, flexible and most of all,
easy to use. Many of the features of Spock are designed to bring
molecular modeling programs into the age of the internet. Spock has
the features users have come to expect from molecular graphics
software including several bond and atom rendering types, and a
complete array of backbone "worm" representations. Further,
Spock can calculate and display molecular and accessible surfaces,
and color code these surfaces by properties (such as electrostatic
potential).
SPSCAN
- a new program to support semi-automatic assignment of
NMR spectra of biological macromolecules. [added 1/18/2001]
Steric
- is a program to calculate the steric size of
molecules about a point
in terms of their cone angles and solid angles, as well as their
total volumes and projected areas.
SwissPDBViewer
- an application that provides a user friendly
interface allowing to
analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare
their active sites or any other relevant parts. Amino acid mutations,
H-bonds, angles and distances between atoms are easy to obtain thanks
to the intuitive graphic and menu interface.
Symmetry
- a set of C codes for automatic molecular symmetry
recognition . Nothing fancy, but can be of use as an analytical or educational
tool. [added 1/13/2001]
TheRate
- an acronym for Theoretical Rates. TheRate allows
thermal rate
constants of unimolecular and bimolecular gas-phase reactions to be
calculated directly from an ab initio and/or density functional
electronic structure theory. The calculations are based on
variational transition state theory augmented by several
multidimensional semiclassical tunneling approximations. TheRate was
designed to be an advanced research tool, as well as a teaching tool
for courses in applied quantum chemistry and kinetics.
Thermo-Calc
- is a powerful and flexible software for all kinds of
thermodynamic
and phase diagram calculations. It is specially designed for systems
with strongly non-ideal phases. It is the only software which can
calculate arbitrary phase diagram sections with up to five
independent variables in multicomponent systems. There are also
facilities to calculate many other types of diagrams for example CVD
depositions, Scheil-Gulliver solidification simulations, partial
pressures in gases etc.
Tinker
- molecular modeling software is a complete and general
package for
MM/MD, with some special features for polypeptides. TINKER has the
ability to use any of several common parameter sets, such as
AMBER-95, CHARMM22, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA.
Parameter sets for other standard force fields such as CHARMM27,
ENCAD, MMFF and UFF are under consideration. In addition, we are
actively developing our own TINKER force field based upon polarizable
atomic multipole electrostatics.
TkRaster3D
- a graphical user interface to the molecular rendering
package Raster3D.
[added 1/18/2001]
Turbomole
- - program package for ab initio Electronic Structure
Calculations.
TURBOMOLE consists of a series of modules; their use is facilitated
by various tools. Outstanding features of TURBOMOLE are: semi-direct
algorithms with adjustable main memory and disk space requirements;
full use of all point groups; efficient integral evaluation; stable
and accurate grids for numerical integration.
TURBO X
- is a graphic tool (TURBO FRODO XViewer) that allows
to model and
manipulate protein and acid nucleic structures. It runs on computers
with bitmap display under X. TURBO X program can be started from a
remote or a local machine. When the local machine is overloaded, user
running clients can arrange for run TURBO X on other hosts. TURBO
Frodo will be available for Linux soon.
"Understanding
Molecular Simulations"
- At this internet site the FORTRAN source code can be
found of Case Studies of the book.
V
- a software package for interactive multidimentional
image/spectral reconstruction, processing and analysis. [added 1/18/2001]
VASP
- a package for performing ab-initio
quantum-mechanical MD using
pseudopotentials and a plane wave basis set. The approach implemented
in VAMP/VASP is based on a finite-temperature local-density
approximation (with the free energy as variational quantity) and an
exact evaluation of the instantaneous electronic ground state at each
MD-step using efficient matrix diagonalization schemes and an
efficient Pulay mixing. The interaction between ions and electrons is
described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector
augmented wave method (PAW). [modified 1/18/2001]
VASP
Data Viewer
- is a scientific visualization package for examining
output files
generated by the Vienna Ab-initio Simulation Package (VASP), a
package for performing ab-initio quantum-mechanical molecular
dynamics using pseudopotentials and a plane wave basis set. The
project was initiated when a chemical engineering professor requested
assitance in visualizing output files produced by the above package.
It displays iso-surfaces and slices of a three-dimensional data set,
along with the atoms that make up the molecule the calculations were
performed for, and allows symbolic bonds to be inserted between
them.
VEGA
- was developed to create a bridge between most of the
molecular
software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac,
etc. In this tool have been also implemented some features that are
useful to analyze, display and manage the 3D structures of molecules.
VEGA is written in high portable code (standard C language) and can
be executed on a lot of hardware systems simply recompiling the
source code.
Vibrate
- is a program for visualizing the normal vibrational
modes of a
molecule. Vibrate can read files generated by Mopac, Gaussian (G92
and G94), and HONDO and display the computed vibrational spectrum.
The user can then select a vibration to display by pointing to one of
the spectral lines and an animated display of the vibrating molecule
will be displayed. Up to four vibrations can be displayed at one time
and the structures can be rotated about any axis. The vibrational
spectrum can be printed along with a vector display of the currently
active vibrational modes.
Viewmol
- is an open source graphical front end for
computational chemistry
programs. It is able to graphically aid in the generation of
molecular structures for computations and to visualize their
results.
VMD
- is designed for the visualization and analysis of
biological systems
such as proteins, nucleic acids, lipid bilayer assemblies, etc. It
may be used to view more general molecules, as VMD can read standard
Protein Data Bank (PDB) files and display the contained structure.
VMD provides a wide variety of methods for rendering and coloring a
molecule: simple points and lines, CPK spheres and cylinders,
licorice bonds, backbone tubes and ribbons, cartoon drawings, and
thers. VMD can be used to animate and analyze the trajectory of a
molecular dynamics (MD) simulation. In particular, VMD can act as a
graphical front end for an external MD program by displaying and
animating a molecule undergoing simulation on a remote computer.
VU
- is a configurable scientific visualization program
for the display and
analysis of numerical solutions. Based on a generic research activity
at CERCA,
its applications range from
CFD to manufacturing, applied mathematics, civil engineering,
computational chemistry.
WebMol
- a Java PDB Viewer. [added 12/30/2000]
WebMol II
- a Java-based 3D viewer for protein structures. [added
1/1/2001]
Weka
- a collection of machine learning algorithms for
solving real-world data mining problems. [added 1/18/2001]
WHAT
IF
- is a versatile protein structure analysis program
that can be used
for mutant prediction, structure verification, molecular graphics,
etc.
WIEN97
- program package allows you to perform electronic
structure
calculations of solids using the full-potential
linearized-augmented-plane-wave (LAPW) method, one among the most
accurate schemes for band structure calculations. It is bare
calculations. It is based on density functional theory and uses the
local (spin) density
approximation (LDA) or the improved version of the generalized
gradient approximation (GGA). It is an all-electron scheme including
relativistic effects.
WinMGM
- is a molecular graphism program. It allow to display
and manipulate
one or more molecules. You can add ribbons, solvent accessible
surface, hydrophobic/electrostatic/custom isopotentials..., use
various display modes. A full screen mode, faster, is also available
(don't say that rendering
is slow if you work only in windowed mode!). A separate command line
program, optimgm2, allow to do energy optimization (Monte-Carlo,
systematic analysis, simplex) and peptide construction.
WMOVIEC
- a program for producing computer animations from
molecular dynamics
simulations, using RCV or COR files. [added 12/30/2000]
WODCA
- World of Computer Assisted Synthesis Planning or
Workbench for the Organization of Data for Chemical Applications is intended
to be used by organic chemists and process chemists that work in the
laboratory. Therefore the developers have aimed to make it as
easy to use as possible. On the other hand, WODCA offers many tools for
planning a synthesis and gives the user great flexibility in switching
from one tool to another. [added 1/13/2001]
XBS
- simple but very useful program for plotting
ball-and-sticks
models of molecules or crystals under the X Window system. By
displaying successive "frames" a kind of movie can be
shown. The program can write Postscript output files. A nice feature
(in my view) is that xbs is controlled by keystrokes and not by
mousing and clicking.
XChemEdit
- package of programs which can draw and edit
three-dimensional
chemical structures, serve as a graphical interface to the GAUSSIAN,
JAGUAR, MOPAC, and BOSS/MCPRO programs, display molecular orbitals,
electron densities, and electrostatic potentials, animate normal mode
vibrations, compute solvent-accessible surface area and volume and
thermochemical properties, and 6) manipulate a variety of common
document formats such as Encapsulated PostScript (EPS) and
FrameMaker.
XCombust
- Who in chemistry did never experience that: You get
your sample back
from the analytical department and look shy onto the elemental
analysis data - and they are way off. So what usually happens is that
one tries to make the numbers fit by postulating solvent inclusion
(like 1 mol of EtOH) and then get stressed out with a desktop
calculator. That's where this tiny shiny utility comes into play.
[added 12/26/2000]
XCrySDen
- Program Purpose: molecular and crystalline structure
render program;
property analyzer; graphical user interface (GUI) for
CRYSTAL95/98program; yields visualization of crystalline structures,
2D/3D electron densitiesand generates k-mesh for band structure plots
for WIEN97program; yields visualization of crystalline structures for
FHI98MD program. [modified 1/9/2001]
XEASY
- is a program to display and assign 2D, 3D, and 4D NMR
spectra.
Evaluation oMR spectra. Evaluation of 3D and 4D spectra is based on
the concept of "strips", i.e. parts of the spectrum the
position of which is defined in a corresponding 2D spectrum. Fully
compatible with DIANA/DYANA (program to calculate 3D structure from
NMR restraints by Peter Güntert).
xelem
- displays a 'hypertext' periodic table. Each element,
when clicked
upon, displays a window with selected data on this element. The data
values can be selected and pasted into other applications. The
standard Tk convention of dragging the middle mouse button allows
scrolling material that overflows its display window. The main
periodic table display shows the element symbol and one additional
value (atomic number, by default) that can be selected via the
'Option/Show' menu. Xelem's claim to fame comes from its
extendability via an ~/.xelemrc initialization file. The extensions
may be as simple as defining new values for data fields.
XEMR
- is a software package written for electron magnetic
resonance (EMR)
spectroscopists. The program consists of the graphical front end
which is written using XForms -library, and the libepr which contains
all the spectrum manipulation and simulation routines.
xite
- consists of display programs with image widget and
graphical user
interface as well as more than 200 command line programs and 600
subroutines for, all documented on-line. XITE uses its own image file
format (BIFF), but comes with converters between BIFF and TIFF, pnm,
sunraster, raw, MATLAB and ascii. [added 1/5/2001]
XLOPG/PLOGP
- is a method which can calculate the logP value for
an organic compound from its topological structure. The algorithm is
based on the summation of atomic contributions and correction
factors. The model was given by the multivariate regression analysis
of 1853 diverse organic compounds. The correlation coefficient of the
whole set fitting was 0.973 and the standard deviation was only 0.35
units. Comparison with other LogP calculation procedures has
demonstrated that XLOGP is much better than other atom-additive
methods and at least comparable to the most popular programs such as
CLOGP.
XMakeMol
- can be used to view and manipulate
atomic and molecular data given in xyz format. XMakemol is a
mouse-based application and many features can be accessed by clicking
or dragging the mouse on the main window. Additional popup dialogs
offer a number of additional features.
XMD
- program which performs Computer Molecular
Dynamics (CMD) simulations on metals and ceramics. [added 1/3/2001] [modified
1/18/2001]
XmMol
- a desktop macromolecular visualization and modeling
tool designed to be easy to use, configure and enhance. Its graphics are based
on X11, and part of its user interface is based on Motif. Thus it provides a
way of displaying structures on any X11 server. [1/13/2001]
XMolCalc
- a small utility that allows you to calculate a
molecular weight
under Unix/X11.
XNMR
- an X11 based program capable of simulating
exchange broadeneating
exchange broadened NMR spectra of dynamic molecules with up to nine
chemical configurations. XNMR further supports up to a certain degree
the processing of experimental data obtained from Bruker NMR
spectrometers running UXNMR or XWin-NMR. An older version can also be
found at ftp://ftp.nmr.de/pub/bruker/nmr/processing/
X-PLOR
- is a system for X-ray crystallography and
NMR.
XPMA
- is a mouse driven menu based graphical program for
the manipulation of crystal structures. It reads SHELX93, SHELXL, SHELX76 and
SHELXS-OUTPUT FILES. [added 1/5/2001] [modified 1/18/2001]
xrs-dist
- comprises a collection of programs for crystal
structural analysis
with powder diffraction data. It provides routines at all levels of
the analysis - examples are Fourier transforms and least-squares
refinements, and also programs to aid in the interpretation and
publication of the refined results. [added 1/5/2001]
Xtal
- a package of over sixty crystallographic programs for
calculations ranging from the reduction of raw diffraction intensities, to the
solution, refinement and publication of crystal structures. These are
applicable to X-ray, neutron and electron diffraction analyses, including
charge density studies. The package contains interactive graphics tools.
[added 1/20/2001]
XtalView
- is a package for X-ray crystal structure solution
from the cture
solution from the point at which data is collected through the
fitting of a molecular model into an electron density map. XtalView
runs on ordinary workstations and does not require 3-D hardware.
Xykron
- is a general-purpose chemical data storage
repository, graphical
editor/front-end and presentation tool. Designed for the practising
research chemist to be able to interactively enter, manipulate and
present data for a variety of chemical compounds. Data include
standard properties, as well as spectroscopy, structural and diagram.
[added 1/3/2001]
xyz2rgb
- makes pretty pictures and movies of molecules. It
expects input in
the form of an XYZ file, one of the file formats frequently used by
computational chemists. As output, it produces one or more
line-interlaced RGB files. These can be converted to other formats
using the ImageMagick image processing toolkit. Conversion between a
wide variety of molecule file formats can be accomplished using a
program called Babel.
YAeHMOP
- is intended to be an easy
to use, transparent, extended Huckel calculation and visualization
package which can perform calculations on both molecular and extended
materials in 1,2, or 3 dimensions.
ZORTEP
- is a mouse driven, menu based graphical ORTEP
program. This allows
the 'real-time' graphical rotation and manipulation of structures
and/or thermal ellipsoids on the screen. [added 1/5/2001]
