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Author Archives: Dan Gezelter
SCORE
SCORE is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Find SCORE at: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html
Posted in Biochemistry
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SeqPup
SeqPup is a biological sequence editor and analysis program. Find SeqPup at: http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/java/
Posted in Bioinformatics
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RnaViz
RnaViz is a user-friendly, portable, GUI 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 … Continue reading
Posted in Biochemistry
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Raster3D
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. Find Raster3D at: http://www.bmsc.washington.edu/raster3d/raster3d.html
Posted in Molecule Viewers and Editors
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PomBase
An AceDB database for the fission yeast Schizosaccharomyces pombe. Find PomBase at: http://www.genedb.org/genedb/pombe/blast.jsp
Posted in Genetics
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QMOL
Qmol is a program for viewing molecular structures and animating molecular trajectories. Find QMOL at: http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml
Posted in Molecule Viewers and Editors
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PyMOL
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. Find PyMOL at: http://pymol.sourceforge.net/
Posted in Molecule Viewers and Editors
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PROCHECK
Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Find PROCHECK at: https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
Posted in Biophysical
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GDPC
gdpc is a program for visualising molecular dynamic simulations Find GDPC at: http://www.frantz.fi/software/gdpc.php
Posted in Molecular Dynamics
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Geanfammer
geanfammer contains divclus which divides proteinclusters into more correct domain level clusters Find Geanfammer at: http://www.mrc-lmb.cam.ac.uk/genomes/geanfammer.html
Posted in Bioinformatics
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