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Nombre del programa
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Distribuidor
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Plataforma de uso
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Funciones del programa
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Alchemy 2000 |
Cherwell Scientific |
Windows 95,98
y NT |
Modelado molecular que incluye
mecánica molecular y visualización para moléculas
pequeñas y macromoléculas. Incluye herramientas de
análisis como
base de datos local, hoja de cálculo y graficación (des) |
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Amber |
School of Pharmacy, Attention:
Elena Jahouach Department of Pharmaceutical Chemistry Mission Bay
Campus University of California UCSF Box
2240 600 16th Street, Room N-457 San Francisco, California 94143-2240
FAX: (415) 514-3866 email: jahouach@cgl.ucsf.edu |
SGI IRIS, LINUX , AMD, IBM-AIX,HP,SUN-OS,MAC-OS,WINDOWS, entre otros
sistemas, |
AMBER refers to two things: a set
of molecular mechanical force fields for the simulation of biomolecules
(which are in the public domain, and are used in a variety of
simulation programs); and a package of molecular simulation programs
which includes source code and demos. The current version of the code
is AMBER version 7, which is
distributed by UCSF subject to a licensing agreement as described below. |
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AmberFFC version
n° 1.3 |
Oxford Molecular |
SGI IRIS, LINUX , AMD, IBM, HP,SUN, MAC, WINDOWS |
Campo de fuerza para la
simulación de biomoléculas |
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BABEL |
University of Arizona |
Unix (AIX, Ultrix, Sun-OS, Convex,
SGI, Cray, Linux),MS-DOS, and Macs running at least System 7.0. |
Babel es un programa
diseñado para interconvertir numerosos archivos a formato de uso
común
en modelado molecular |
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| CHARMM |
Harvard University |
UNIX (Fortran) |
Mecánica y dinámica
molecular para macromoléculas |
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Chimera |
UCSF |
FreeBSD, mac OSX, HPTRU64, SGI IRIX, Linux 64, Linux,
winwods |
UCSF Chimera is a highly extensible program for interactive visualization
and analysis of molecular structures and related data, including density
maps, supramolecular assemblies, sequence alignments, docking results,
trajectories, and conformational ensembles. High-quality images and
animations can be generated. |
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CORINA
|
molecular-networksGmbh |
SGI (R4400), IRIX 5.3 |
A rule and data based system, that
automatically generates three-dimendional atomic coordinates from the
constitution of a molecule as expressed by a connection table, powerful
and reliable to convert large data bases or several hundreds of
thoysand
or even million of compounds. |
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DelPhi
(versión académica) |
Columbia University |
Código fuente
(Unix, Linux, Pc, IBM de AIX, Mac) |
Soluciona la ecuación de
Poisson-Boltzmann, que es usada para obtener campos
electrostáticos y potenciales
de biomoléculas. Calcula energías de enlace de
fármacos potenciales que pueden ser rediseñados para una
unión óptima con la biomolécula blanco. |
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DL_POLY |
Daresbury Laboratory, UK |
Código fuente |
Paquete de simulación de
dinámica molecular paralelo. |
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Dock |
UCSF |
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predict binding modes of small molecule-protein
complexes,search databases of ligands for compounds that inhibit enzyme
activity, search databases of ligands for compounds that bind a particular
protein, search databases of ligands for compounds that bind nucleic acid
targets, examine possible binding orientations of protein-protein and
protein-DNA complexes, help guide synthetic efforts by examining small
molecules that are computationally derivatized, |
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Fantom |
University of Texas Medical Branch
at Galveston, Human Biological Chemistry and Genetics Department |
Código fuente para UNIX |
Calcula conformaciones de
polipéptidos y proteínas de baja energía
conformacional con restricciones de experimentos de RMN. Además,
modelado molecular. |
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GETAREA 1.1 |
University of Texas Medical Branch
at Galveston, Sealy Center for Structural Biology |
Código fuente para UNIX |
Calcula el área de
superficie accesible en solventes, energia de solvatación
atómica y
los gradientes para macromoléculas |
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| GMMX |
Serena Software |
Windows, MacOS X,
Linux, Unix
versions available upon request |
Minimización de
energía estérica con el campo de fuerza MMX |
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| Gromacs 3 |
University of Groningen |
Linux, código fuente en C |
Dinámica molecular en
paralelo |
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GROMOS |
Cray Research, Inc. |
UNICOS/Cray |
Dinámica molecular para el
estudio de sistemas biomoleculares cuyo propósito es simular
moléculas arbitrarias en solución o en estado cristalino
por dinámica molecular o dinámica estocástica |
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| Hingefind |
University of Illinois at
Urbana-Champaign |
UNIX |
Programa para investigar
movimientos de dominios en proteínas |
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| HyperChem |
Hypercube, Inc. |
Windows |
Mecánica molecular |
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Hyperchem 8.0 Professional |
chemistry-software |
Windows
vista, xp |
HyperChem is a sophisticated molecular modeling environment that is known
for its quality, flexibility, and ease of use. Uniting 3D visualization
and animation with quantum chemical calculations, molecular mechanics, and
dynamics |
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ICM |
Molsoft, LLC. |
SGI, Linux, Mac
Os, Windows |
Modelado molecular y
optimización de geometrías en sistemas multimoleculares
colocados arbitrariamente. Predicción de rearreglos moleculares
en biopolímeros |
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Insight 11 |
Molecular Simulations |
Linux |
Modelado molecular |
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Interchem |
Interprobe Chemical Services |
SGI |
Modelado molecular con
mecánica molecular y cuántica para sistemas
pequeños y grandes |
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MacroModel
7 |
Department of Chemistry, Columbia
University and has now moved to Schrödinger, Inc |
SGI, IBM RS/6000, X |
Modelado de moléculas
orgánicas y bioorgánicas. Mecánica y
dinámica molecular |
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ModelMaker |
ModelKinetix |
Windows |
Es un poderoso sistema de ventanas
para diseñar, analizar y modelar procesos y sistemas. |
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| Molecular
Operating Environment (MOE) |
chemical Computing Group INC. |
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MOE shall be a computerizad
enviroment dedicated to computational chemistry and bioinformatics in
which scientific methodology can be rapidly protetyped, experimented
with, verifier, deployed and effectively used. |
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Moldy |
keith Refson, University Research
Assistant in mineral Physics. |
UNIX, PCs |
Es un programa que tiene el
propósito de hacer simulaición por dinámica
molecular. |
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Molecular Modeling Pro |
chemistry-software |
windows |
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Molecular
Modelling Toolkit (MMTK) |
Python |
Mac |
The Molecular Modelling Toolkit
(MMTK) is a program library for molecular modelling applications. Its
aim is
to provide researchers, especially those working on the development of
new modelling methods, with a code basis that can be easily extended
and
modified to deal with standard and non-standard problems in molecular
modelling. |
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Moilin |
Crystallography Centre
National University of Ireland, Galway, University Road, Galway, Ireland |
windows |
Moilin will work in stand alone mode or under Oscail |
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| MM3,
MM4 |
QCPE |
IBM RS/6000 (aix), SGI (irix),
Digital Alpha (osf), DEC (ultrix), Linux |
Mecánica molecular/Allinger
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| Modeller |
Lab of Molecular Biophysics at
Rockefeller University |
UNIX |
Programa para homología y
modelado comparativo de estructura tridimensional protéica |
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MOIL-9.0 |
University of California at San
Francisco |
Windows, Unix |
Programa para visualizar y
analizar estructuras, y dinámica molecular |
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Molgen-Ms |
Universität Bayreuth |
Windows Nt,2000 |
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Molgen |
Universität Bayreuth |
C, C++, OS/2, Windows,
SUN Solaris/Motif |
Elucidación de estructura
química: generador de isómeros configuracionales,
minimización por mecánica molecular |
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MOLGEN |
CCL |
DOS |
Elucidación de estructura
química: generador de isómeros configuracionales,
minimización por mecánica molecular |
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MOPAC2007 |
CAChe Research |
LINUX, WINDOWS |
is a semiempirical quantum chemistry software package for the prediction
of chemical properties and modeling of chemical reactions. It is used by
chemists and biochemists for both research and teaching, |
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MSI Web Lab
Viewer |
WebLab |
PC, Macintosh, UNIX |
MSI es un método para
simular via browsera de World Wide Web |
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NAB |
Scripps Research Institute |
UNIX,
linux, mac OX, windows |
Lenguaje de manipulación:
modelado de ácidos nucléicos |
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| NAMD |
Theoretical Biophysics Group,
Beckman Institute |
Código fuente en C++ |
Dinámica molecular:
paralelo, orientado a objetos, para simulaciones de sistemas
moleculares biológicos |
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Nemesis |
Oxford Molecular |
Windows, Mac |
Modelado molecular,
búsquedas conformacionales |
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NWChem |
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory |
Linux, Mac |
Biomolecules, nanostructures, and solid-state
From quantum to classical, and all combinations
Gaussian basis functions or plane-waves
Scaling from one to thousands of processors
Properties and relativity |
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| PCMODEL |
Serena Software |
SGI |
Modelado molecular |
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PKanalyst |
MicroMath Scientific Software |
Windows |
se diseño para simular y realizar la valoración de
parámetros para los modelos farmacocineticos |
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Quanta - CHARMm |
Molecular Simulations |
SGI |
Modelado molecular |
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Sculpt |
MDL |
SGI, Mac |
Modelado molecular,
simulación y diseño de fármacos |
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| Spartan
|
Wavefunction Inc. |
Windows,Linux, Mac, unix |
Modelado molecular, incluye
mecánica molecular |
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| STR3DIMW |
Exorga, Inc. |
DOS, Windows |
Modelado molecular con campo de
fuerza QVBMM para moléculas bioorgánicas como
sacáridos, amino ácidos, nucleósidos y sus
polímeros |
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Sybyl |
Tripos |
LInux, Iris, |
Modelado molecular |
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| TINKER |
Washington University School of
Medicine in St. Louis, Missouri |
linux, windows,macOs, Código fuente en fortran 77 |
Mecánica molecular con los
potenciales de MM2, MM3, AMBER-95, AMBER/OPLS, CHARMM22 y el propio de
TINKER. Dinámica molecular |
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Trident |
Wavefuntion, inc. |
Windows 2000. xp |
Calculate and analyze molecular structures, energies, and properties |
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| VMD (Visual Molecular
Dynamics) |
Beckman Institute |
MacOs,Unix,Windows |
Dinámica molecular:
visualización y análisis. |
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Xmol ver 1.2 |
Network Computing Sevices, Inc. |
DEC Alpha, SGI IRIS-4d, IBM
RS/6000, Linux Windows y Macintosh |
Paquete de modelado molecular en
3D con animaciones y cálculos de distancias entre átomos,
ángulos de enlace y ángulos torsionales |
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| Yak |
Swiss Federal Institute of
Technology, ETH Zürich |
UNIX |
Modelado con seudo-bioreceptor:
con el concepto de seudoreceptor se construye un modelo de receptor que
imite las interacciones ligando macromolécula |
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VIDA & VIVANT |
Openeye |
unix, linux, mac, windows |
Molecular modeling is more than just generating numbers. It
is about understanding, rationalizing, predicting, and, most importantly,
communicating results. VIDA creates visual content by allowing the modeler
to make live, interactive 3D views, annotated with important details, and
organized in preset, "bookmarked" scenes. VIVANT "publishes" this content
in a variety of media, including PowerPoint® , Word® and web pages. By
lowering the barriers to communication and providing cutting edge graphics
and science to all, VIDA and VIVANT bring the big picture home. |
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