|
|
Sequence
Analysis:
|
|
|
|
|
BioEdit |
Windows |
|
BioEdit is a full integrated
sequence/alignment editor. Performs translations, phylogenetic
analysis, clustalw alignments, ABI trace analysis, RNA
comparative analysis and BLAST searches.
|
|
URL:
http://www.mbio.ncsu.edu/BioEdit/bioedit.html |
|
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|
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BLAST |
Linux
|
Windows |
|
BLAST 2.0, (Basic Local Alignment
Search Tool), provides a method for rapid
searching of nucleotide and protein databases.
|
|
URL:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/ |
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BOXSHADE |
Linux |
|
BOXSHADE is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does no
alignment by itself, it has to take as input a file preprocessed
by a multiple alignment program or a multiple file editor.
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URL:
ftp://www.isrec.isb-sib.ch/pub/ |
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TOP |
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Circle |
Windows |
Infer RNA secondary structure using the
comparative method.
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|
URL:
http://taxonomy.zoology.gla.ac.uk/rod/circles/ |
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TOP |
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ClustalW |
Linux
|
Windows |
Clustal-W is a multiple sequence
alignment program. It provides an integrated environment for
performing multiple sequence and profile alignments and
analyzing the results.
|
|
URL:
ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ |
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TOP |
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ClustalX |
Linux
|
Windows |
|
ClustalX is a new windows interface for the
ClustalW. It provides an integrated environment for performing
multiple sequence and profile alignments and analyzing the
results.
|
|
URL:
ftp://ftp.ebi.ac.uk/pub/software/dos/clustalx/ |
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TOP |
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Dambe |
Windows |
It is a general-purpose package for DNA and
protein sequence phylogenies, and also gene frequencies.
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|
URL:
http://aix1.uottawa.ca/~xxia/software/software.htm |
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TOP |
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DCSE |
Linux
|
Windows |
|
DCSE (Dedicated Comparative Sequence Editor) is
a multiple alignment editor. It can be used to edit protein, DNA
or RNA alignments. The structure of the molecules can be
incorporated in the alignment.
|
|
URL:
http://rrna.uia.ac.be/dcse/ |
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TOP |
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DNA Tools |
Windows |
|
DNATools is a comprehensive program
package for routine handling and analysis of nucleotide and
protein sequences. The program includes functions for batch
renaming, editing and annotating sequences, restriction mapping,
translation, automated blast search and information retrieval, codon analysis, primer design and ordering and a lot more...
|
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URL:
http://www.crc.dk/dnatools/ |
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TOP |
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DNA Club |
Windows |
PC program for Integrated analysis on DNA
sequences.
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|
URL:
http://softwareseek.progenote.net/downloads/ |
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TOP |
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EMBOSS |
Linux
|
Windows |
|
EMBOSS, The European Molecular Biology
Open Source Software Suite, is a
package of high-quality FREE Open Source software for sequence
analysis.
|
|
URL:
http://emboss.sourceforge.net/ |
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TOP |
|
FastA |
Linux
|
Windows |
|
The FastA
program has been developed by Pearson & Lipman (1988) and is
useful to find all protein sequences of a database such as
Swiss-Prot, that are homologous to a given sequence.
|
|
URL:
http://www.ebi.ac.uk/fasta33/ |
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TOP |
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FreeTree |
Windows |
Freeware program
for construction and bootstrap (and jackknife) analysis of
phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)
|
|
URL:
http://www.natur.cuni.cz/~flegr/programs/freetree.htm |
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TOP |
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GeneDoc |
Windows |
GeneDoc does sequence alignment editing and
shading, as well as secondary structure shading and super family
group support.
|
|
URL:
http://www.psc.edu/biomed/genedoc/ |
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TOP |
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GeneTree |
Windows |
|
GeneTree is an experimental program for comparing gene and
species trees.
|
|
URL:
http://www.stats.ox.ac.uk/~griff/software.html |
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TOP |
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HMMER |
Linux |
|
A profile hidden Markov model that can be used to
do sensitive database searching using statistical descriptions
of a sequence family's consensus.
|
|
URL:
http://hmmer.wustl.edu/ |
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TOP |
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HyPhy |
Windows |
|
It intended to perform maximum likelihood analyses of genetic
sequence data and equipped with tools to test various
statistical hypotheses. HYPHY was designed with maximum
flexibility in mind and to that end it incorporates a simple
high level programming language which enables the user to tailor
the analyses precisely to his or her needs. These include
relative rate and ratio tests, several methods of ML based
phylogeny reconstruction, bootstrapping, model selection,
positive selection, molecular clock tests and many more...
|
|
URL:
http://www.hyphy.org/ |
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|
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TOP |
|
JalView |
Linux
|
Windows |
|
Graphical multiple alignment editor. Requires
Java Virtual Machine.
|
|
URL:
http://www.jalview.org/ |
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TOP |
|
JEMBOSS |
Windows |
|
Jemboss is developed by the EMBOSS team. The software is free
and part of the EMBOSS distribution.
|
|
URL:
http://emboss.sourceforge.net/Jemboss/ |
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TOP |
|
Mega3 |
Windows |
|
MEGA is an integrated tool for automatic and manual
sequence alignment, inferring phylogenetic trees, mining
web-based databases, estimating rates of molecular evolution,
and testing evolutionary hypotheses.
|
|
URL:
http://www.megasoftware.net/ |
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TOP |
|
MFold |
Linux |
|
Mfold is an RNA and DNA folding package.
|
|
URL:
http://www.bioinfo.rpi.edu/~zukerm/export/mfold-3.html |
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TOP |
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NCBI ToolKit |
Linux
|
Windows |
|
The
NCBI Software Development Toolkit was developed for the
production and distribution of GenBank, Entrez, BLAST, and
related services by NCBI.
|
|
URL:
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ |
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TOP |
|
PHYLIP |
Linux
|
Windows |
|
PHYLIP is a free package of
programs for inferring phylogenies.
|
|
URL:
http://evolution.genetics.washington.edu/phylip.html |
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|
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TOP |
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PhyloDraw |
Windows |
|
PhyloDraw is a drawing tool for creating phylogenetic
trees. It supports various kinds of multialignment programs
(Dialign2, Clustal-W, Phylip format, and pairwise distance
matrix) and visualizes various kinds of tree diagrams.
|
|
URL:
http://pearl.cs.pusan.ac.kr/phylodraw/ |
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|
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TOP |
|
RNA DRAW |
Windows |
|
It is an integrated program for RNA secondary structure
calculation and analysis.
|
|
URL:
http://www.rnadraw.com/ |
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|
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TOP |
|
Readseq |
Windows |
|
Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
|
|
URL:
http://iubio.bio.indiana.edu/soft/molbio/readseq/ |
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|
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TOP |
|
Seaview |
Linux
|
Windows |
SeaView is a
graphical multiple sequence alignment editor. It is able to
read and write various alignment formats (NEXUS, MSF, CLUSTAL,
FASTA, PHYLIP, MASE). It allows to manually edit the alignment,
and also to run DOT-PLOT or CLUSTALW programs to locally improve
the alignment.
|
|
URL:
http://pbil.univ-lyon1.fr/software/seaview.html |
|
|
|
TOP |
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Sequence Manipulation Suite |
Linux
|
Windows |
|
The Sequence Manipulation Suite is a collection of JavaScript
programs for generating, formatting, and analyzing short DNA and
protein sequences. It is commonly used by molecular biologists,
for teaching, and for program and algorithm testing.
|
|
URL:
http://bioinformatics.org/sms2/ |
|
|
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TOP |
|
TreeView |
Linux
|
Windows |
|
TreeView X is an open source program to display phylogenetic
trees. It can read and display NEXUS and Newick format tree
files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and
other programs).
|
|
URL:
http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.html |
|
|
|
TOP |
|
Vienna RNA Package |
Linux
|
Windows |
|
RNA Secondary Structure Prediction and Comparison.
|
|
URL:
http://www.tbi.univie.ac.at/~ivo/RNA/ |
|
|
|
TOP |
|
WinGene |
Windows |
|
A
tool for the analysis of nucleotide sequences.
|
|
URL:
http://www.ipw.agrl.ethz.ch/~lhennig/wingene.html |
|
|
|
TOP |
|
X3DNA |
Linux
|
Windows |
|
3DNA
is a versatile package for analyzing and rebuilding
three-dimensional nucleic acid structures, based on a
standard reference frame.
|
|
URL:
http://rutchem.rutgers.edu/~xiangjun/3DNA/ |
| |
|
TOP |
Genomics:
|
|
|
|
|
Artemis |
Linux
|
Windows |
|
Artemis is a free
genome viewer and annotation tool that allows visualization of
sequence features and the results of analyses within the context
of the sequence, and its six-frame translation.
|
|
URL:
http://www.sanger.ac.uk/Software/Artemis/ |
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|
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TOP |
|
Chromas |
Windows |
|
It will display and prints chromatogram files
from ABI automated DNA sequencers, and Staden SCF files which
the analysis programs for ALF, Li-Cor and Visible Genetics
OpenGene sequencers can create.
|
|
URL:
http://www.technelysium.com.au/chromas.html |
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|
|
TOP |
|
GenAl |
Linux |
|
GenAl is a program for genomic alignment, i.e. alignment of DNA
sequences with coding regions. It is an implementation of the
heuristic algorithm described in Hein, J. & J. Stoevlbaek
(1994): Genomic Alignment. J. Mol. Evol.
|
|
URL:
ftp://ftp.ebi.ac.uk/pub/software/unix/ |
|
|
|
TOP |
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Glimmer |
Linux |
|
A
system for finding genes in microbial DNA, especially the
genomes of bacteria and archaea.Glimmer (Gene Locator and
Interpolated Markov Modeler) uses interpolated Markov models (IMMs)
to identify the coding regions and distinguish them from
noncoding DNA.
|
|
URL:
http://www.tigr.org/software/glimmer/ |
|
|
|
TOP |
|
Glimmer HMM |
Linux |
|
A fast and accurate gene finder based on a GHMM architecture,
developed specifically for eukaryotes. It incorporates splice
site models adapted from the GeneSplicer program and uses
interpolated Markov models for evaluating the coding regions.
|
|
URL:
http://www.tigr.org/software/GlimmerHMM/ |
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|
|
TOP |
|
Glimmer M |
Linux |
|
A
gene finder derived from Glimmer, but developed specifically for
eukaryotes. It is based on a dynamic programming algorithm that
considers all combinations of possible exons for inclusion in a
gene model and chooses the best of these combinations. The
decision about what gene model is best is a combination of the
strength of the splice sites and the score of the exons
generated by an interpolated Markov model (IMM).
|
|
URL:
http://www.tigr.org/software/glimmerm/ |
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|
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TOP |
|
MUMmer |
Linux |
|
MUMmer is a system for rapidly aligning entire genomes, whether
in complete or draft form.
|
|
URL:
http://www.tigr.org/software/mummer/ |
|
|
|
|
|
pDRAW |
Windows |
|
pDRAW32 is being developed as a
free time hobby project. It is far from finished, but as it has
reached a point where it could be helpful for many labs, it is
now available to the scientific community.
|
|
URL:
http://www.acaclone.com/ |
|
|
|
TOP |
|
PrimerDesign |
Linux
|
Windows |
|
Primer Design is a DOS-program to choose primer for PCR or
oligonucleotide probes. It is tailored to check known sequences
for repeats and unique sequences and subsequently to create
prober primers according to this data. A lot of constrains are
available to meet your conditions. It can handle up to 32000
base pairs.
|
|
URL:
http://www.bioinf-club.com/software/ |
|
|
|
TOP |
|
Sequin |
Linux
|
Windows |
|
Sequin is a stand-alone software tool developed by the NCBI for
submitting and updating entries to the GenBank, EMBL, or DDBJ
sequence databases. It is capable of handling simple submissions
that contain a single short mRNA sequence, and complex
submissions containing long sequences, multiple annotations,
segmented sets of DNA, or phylogenetic and population studies.
|
|
URL:
http://www.ncbi.nlm.nih.gov/Sequin/ |
|
|
|
TOP |
|
Staden |
Linux
|
Windows |
|
The Staden Package consists of a series of tools for DNA
sequence preparation (pregap4), assembly (gap4), editing (gap4)
and DNA/protein sequence analysis (spin).
|
|
URL:
http://staden.sourceforge.net/ |
|
|
|
TOP |
Proteomics:
Systems Biology:
|
|
|
|
|
Cellware |
Linux
|
Windows |
|
Cellware has been designed to conduct modeling and simulation of
gene regulatory and metabolic pathways and also offer an
integrated environment for diverse mathematical representations,
parameter estimation and optimization. In addition, a
user-friendly graphical display and capability to run large and
complex models would be provided by default. A very special
feature of Cellware is that it would be the first grid based
modeling and simulation tool in the field of Systems Biology.
|
|
URL:
http://www.bii.a-star.edu.sg/research/sbg/cellware/ |
|
|
|
TOP |
|
CytoScape |
Linux
|
Windows |
|
Cytoscape is a visualization platform for use with molecular
interaction networks. Interaction data can be integrated with
other state data such as gene expression profiles. The input to
Cytoscape includes lists of interaction pairs, and tab/space
delimited files containing mRNA expression profiles. The nodes
of the interaction networks can be filtered by such variables as
GO annotations and number of interactions.
|
|
URL:
http://www.cytoscape.org/ |
|
|
|
TOP |
|
E-Cell 3 |
Linux
|
Windows |
|
E-Cell Project is an international research project aiming to
model and reconstruct biological phenomena in silico, and
developing necessary theoretical supports, technologies and
software platforms to allow precise whole cell simulation.
|
|
URL:
http://www.e-cell.org/ |
|
|
|
TOP |
|
Gepasi |
Linux
|
Windows |
|
Gepasi is a software package for modeling biochemical systems.
It simulates the kinetics of systems of biochemical reactions
and provides a number of tools to fit models to data, optimize
any function of the model, perform metabolic control analysis
and linear stability analysis.
|
|
URL:
http://www.gepasi.org/ |
|
|
|
TOP |
Molecular
Modeling:
|
|
|
TOP |
|
3D-Dock Suite |
Linux |
|
[FTDock,
RPScore and MultiDock]
FTDock ( Fourier Transform Dock ) performs rigid-body docking on
two biomolecules in order to predict their correct binding
geometry. FTDock outputs multiple predictions that can be
screened using biochemical information.
|
|
URL:
http://www.bmm.icnet.uk/docking/ |
|
|
|
TOP |
|
ArgusLab |
Windows |
|
It is an incredible molecular
modeling, graphics, and drug design program.
|
|
URL:
http://www.planaria-software.com/ |
|
|
|
TOP |
|
Biodesigner |
Windows |
|
It
is a molecular modeling and visualization program for personal
computers which is capable of creating homologous models of
proteins, evaluate, and refine the models.
|
|
URL:
http://www.pirx.com/biodesigner/index.shtml |
|
|
|
TOP |
|
Chem2Pac |
Windows |
|
Chem2Pac is intended to be a kind of computational chemistry
integrator, which has a multiple document interface, a molecular
rendering utility, and allows the manipulation of various files.
|
|
URL:
http://www.ifi.unicamp.br/gsonm/chem2pac/ |
|
|
|
TOP |
|
Cn3D |
Linux
|
Windows |
|
Cn3D is a
helper application for your web browser that allows you to view
3-dimensional structures from NCBI's
Entrez
retrieval service.
|
|
URL:
http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml |
|
|
|
TOP |
|
Dang |
Linux |
|
Dang reads coordinates from a Protein DataBank (PDB) molecular
structure file and generates a table of several useful geometric
measurements for each residue or base. In its most basic form,
it writes out dihedral angles (phi, psi, chi) hence the name.
The output is formatted for easy parsing by awk, grep, sort and
other UNIX utilities.
|
|
URL:
http://kinemage.biochem.duke.edu/software/dang.php |
|
|
|
TOP |
|
DomainFinder |
Linux |
|
It is an interactive program for the determination and
characterization of dynamical domains in proteins. Its key
features are computational efficiency: even large proteins can
be analyzed using a desktop computer in a few minutes ease of
use: a state-of-the-art graphical user interface export of
results for visualization and further analysis (VRML, PDB, and
MMTK object format).
|
|
URL:
http://dirac.cnrs-orleans.fr/DomainFinder/ |
|
|
|
TOP |
|
Easy Winbabel |
Windows |
|
It's a program for chemists and physicists dealing with
molecular modeling. It uses the well known BABEL program as
basis and provides a windows interface. The zip file includes
BABEL ver 1.6.
|
|
URL:
http://users.uoi.gr/nkourkou/babel.html |
|
|
|
TOP |
|
EDPDB |
Linux
|
Windows |
|
EdPDB is a program to manipulate and extract information from
Brookhaven Protein Databank (PDB) format coordinate file(s) of
three-dimensional protein structures.
|
|
URL:
http://omega.omrf.ouhsc.edu/zhangc/edpdb/edpdb.html |
|
|
|
TOP |
|
Garlic |
Linux |
|
It
is a free molecular visualization program, protein structure,
DNA structure, PDB, molecular rendering, biological
macromolecule, unix, linux, free software download, open source
software.
|
|
URL:
http://garlic.mefos.hr/garlic-1.0/ |
|
|
|
TOP |
|
Ghemical |
Linux |
|
Ghemical is a computational chemistry software package released
under the GNU GPL. Geometry optimization, molecular dynamics and
some visualization tools are currently available. If
quantum-mechanical calculations are needed, Ghemical can be
directly linked into the quantum chemistry program MPQC (which
is also distributed under GNU GPL). Therefore Ghemical can serve
as a graphical front-end for the MPQC program, currently
providing various 3D-plots for electron densities, molecular
orbitals and molecular orbital densities.
|
|
URL:
http://www.uku.fi/~thassine/ghemical/ |
|
|
|
TOP |
|
gOpenMol |
Linux
|
Windows |
|
gOpenMol graphics interface to the OpenMol and can be used for
the analysis and display of molecular dynamics trajectories and
the display of molecular orbital's, electron densities and
electrostatic potentials.
|
|
URL:
http://www.csc.fi/gopenmol/ |
|
|
|
TOP |
|
GRAMM |
Linux |
|
GRAMM is a program for protein docking. To predict the structure
of a complex, it requires only the atomic coordinates of the two
molecules (no information about the binding sites is needed).
The program performs an exhaustive 6-dimensional search through
the relative translations and rotations of the molecules. The
molecular pairs may be: two proteins, a protein and a smaller
compound, two transmembrane helices, etc. GRAMM may be used for
high-resolution molecules, for inaccurate structures (where only
the gross structural features are known), in cases of large
conformational changes, etc.
|
|
URL:
http://www.chem.ac.ru/Chemistry/Soft/GRAMM.en.html |
|
|
|
TOP |
|
GROMACS |
Linux
|
Windows |
|
GROMACS is a
versatile package to perform molecular dynamics, i. | | |
