AlgoBox

source : http://www.xm1math.net/algobox/exemples/vigenere.html

Dans le cadre de la  MPS  Police scientifique , on peut faire de la  cryptologie et codage :Cryptage affine avec EXCEL...
On peut utiliser aussi AlgoBox :
AlgoBox est un logiciel libre, multi-plateforme et gratuit d'aide à l'élaboration et à l'exécution d'algorithmes dans l'esprit des nouveaux programmes de mathématiques du lycée.
Cryptage d'un message par le chiffre de Vigenere
Présentation de l'algorithme :
Principe :
Le chiffre de Vigenere utilise une clef que l'on répéte autant de fois que nécessaire afin d'avoir la même longueur que le message à crypter. Exemple avec comme message "LEMESSAGEACRYPTER" et comme clef "MACLEF" :
LEMESSAGEACRYPTER
MACLEFMACLEFMACLE
La lettre de la clef figurant dans la deuxième ligne indique le décalage à apporter à la lettre du message située au dessus. Exemple :
Si la lettre de la clef est un A, on ne décale pas la lettre correspondante du message;
Si la lettre de la clef est un B, on décale d'un rang dans l'alphabet la lettre correspondante du message : ainsi un A dans le message devient un B, un B devient un C, etc...
Si la lettre de la clef est un C, on décale de 2 rangs dans l'alphabet la lettre correspondante du message : ainsi un A dans le message devient un C, un B devient un D, etc...
etc...
Cet exemple : la première lettre du message est un L; la lettre correspondante de la clef est un M qui représente un décalage de 12. La première lettre du message crypté est donc un X (12 lettres plus loin que L dans l'alphabet).
Note : Si après décalage, on dépasse la fin de l'alphabet, on continue à compter en repartant du début de l'alphabet. C'est pour cela qu'on peut aussi utiliser une grille appelée "carré de Vigenere" .

Application avec l'algorithme (simplifié) ci-dessous qui ne convient que si le message et la clef ne comportent que des lettres majuscules de A à Z sans espaces.
(note technique : l'instruction message.charCodeAt(pos) permet d'obtenir le code ASCII de la lettre située à la position "pos" dans la chaine "message" et l'instruction String.fromCharCode(un_nombre) renvoie la lettre dont le code ASCII correspond à "un_nombre")

http://www.xm1math.net/algobox/exemples/vigenere.html

vigenere.alg
source du fichier :

<?xml version="1.0" encoding="UTF-8"?>
<Algo>
    <description texte="Cryptage d'un message par le chiffre de Vigenere : le message et la clef ne doivent comporter que des lettres majuscules de A à Z sans espaces." courant="FIN_ALGORITHME" />
    <fonction fctcode="" fctetat="inactif" />
    <repere repetat="inactif" repcode="-10#10#-10#10#2#2" />
    <item algoitem="VARIABLES" code="100#declarationsvariables" >
        <item algoitem="message EST_DU_TYPE CHAINE" code="1#CHAINE#message" />
        <item algoitem="longueur_message EST_DU_TYPE NOMBRE" code="1#NOMBRE#longueur_message" />
        <item algoitem="clef EST_DU_TYPE CHAINE" code="1#CHAINE#clef" />
        <item algoitem="longueur_clef EST_DU_TYPE NOMBRE" code="1#NOMBRE#longueur_clef" />
        <item algoitem="i EST_DU_TYPE NOMBRE" code="1#NOMBRE#i" />
        <item algoitem="code_lettre EST_DU_TYPE NOMBRE" code="1#NOMBRE#code_lettre" />
        <item algoitem="decalage EST_DU_TYPE NOMBRE" code="1#NOMBRE#decalage" />
        <item algoitem="lettre EST_DU_TYPE CHAINE" code="1#CHAINE#lettre" />
    </item>
    <item algoitem="DEBUT_ALGORITHME" code="101#debutalgo" >
        <item algoitem="LIRE message" code="2#message#pasliste" />
        <item algoitem="LIRE clef" code="2#clef#pasliste" />
        <item algoitem="longueur_message PREND_LA_VALEUR message.length" code="5#longueur_message#message.length#pasliste" />
        <item algoitem="longueur_clef PREND_LA_VALEUR clef.length" code="5#longueur_clef#clef.length#pasliste" />
        <item algoitem="POUR i ALLANT_DE 1 A longueur_message" code="12#i#1#longueur_message" >
            <item algoitem="DEBUT_POUR" code="13#debutpour" />
            <item algoitem="code_lettre PREND_LA_VALEUR message.charCodeAt(i-1)-65" code="5#code_lettre#message.charCodeAt(i-1)-65#pasliste" />
            <item algoitem="decalage PREND_LA_VALEUR clef.charCodeAt((i-1)%longueur_clef)-65" code="5#decalage#clef.charCodeAt((i-1)%longueur_clef)-65#pasliste" />
            <item algoitem="lettre PREND_LA_VALEUR String.fromCharCode(65+(code_lettre+decalage)%26)" code="5#lettre#String.fromCharCode(65+(code_lettre+decalage)%26)#pasliste" />
            <item algoitem="AFFICHER lettre" code="3#lettre#0#pasliste" />
            <item algoitem="FIN_POUR" code="14#finpour" />
        </item>
    </item>
    <item algoitem="FIN_ALGORITHME" code="102#finalgo" />
</Algo>

 

Le cryptage affine, on peut utiliser le site :

Pour vous aider, vous pouvez utiliser le lien suivant qui permet de faire l'analyse fréquentielle d'un texte simple : Fréquence des lettres d’un texte ou directement l’adresse http://www.cryptage.org/outil-crypto-frequences.html

 

 

source : http://www.xm1math.net/algobox/exemples/vigenere.html

Dans le cadre de la  MPS  Police scientifique , on peut faire de la  cryptologie et codage :Cryptage affine avec EXCEL...
On peut utiliser aussi AlgoBox :
AlgoBox est un logiciel libre, multi-plateforme et gratuit d'aide à l'élaboration et à l'exécution d'algorithmes dans l'esprit des nouveaux programmes de mathématiques du lycée.
Cryptage d'un message par le chiffre de Vigenere
Présentation de l'algorithme :
Principe :
Le chiffre de Vigenere utilise une clef que l'on répéte autant de fois que nécessaire afin d'avoir la même longueur que le message à crypter. Exemple avec comme message "LEMESSAGEACRYPTER" et comme clef "MACLEF" :
LEMESSAGEACRYPTER
MACLEFMACLEFMACLE
La lettre de la clef figurant dans la deuxième ligne indique le décalage à apporter à la lettre du message située au dessus. Exemple :
Si la lettre de la clef est un A, on ne décale pas la lettre correspondante du message;
Si la lettre de la clef est un B, on décale d'un rang dans l'alphabet la lettre correspondante du message : ainsi un A dans le message devient un B, un B devient un C, etc...
Si la lettre de la clef est un C, on décale de 2 rangs dans l'alphabet la lettre correspondante du message : ainsi un A dans le message devient un C, un B devient un D, etc...
etc...
Cet exemple : la première lettre du message est un L; la lettre correspondante de la clef est un M qui représente un décalage de 12. La première lettre du message crypté est donc un X (12 lettres plus loin que L dans l'alphabet).
Note : Si après décalage, on dépasse la fin de l'alphabet, on continue à compter en repartant du début de l'alphabet. C'est pour cela qu'on peut aussi utiliser une grille appelée "carré de Vigenere" .

Application avec l'algorithme (simplifié) ci-dessous qui ne convient que si le message et la clef ne comportent que des lettres majuscules de A à Z sans espaces.
(note technique : l'instruction message.charCodeAt(pos) permet d'obtenir le code ASCII de la lettre située à la position "pos" dans la chaine "message" et l'instruction String.fromCharCode(un_nombre) renvoie la lettre dont le code ASCII correspond à "un_nombre")

http://www.xm1math.net/algobox/exemples/vigenere.html

vigenere.alg
source du fichier :

<?xml version="1.0" encoding="UTF-8"?>
<Algo>
    <description texte="Cryptage d'un message par le chiffre de Vigenere : le message et la clef ne doivent comporter que des lettres majuscules de A à Z sans espaces." courant="FIN_ALGORITHME" />
    <fonction fctcode="" fctetat="inactif" />
    <repere repetat="inactif" repcode="-10#10#-10#10#2#2" />
    <item algoitem="VARIABLES" code="100#declarationsvariables" >
        <item algoitem="message EST_DU_TYPE CHAINE" code="1#CHAINE#message" />
        <item algoitem="longueur_message EST_DU_TYPE NOMBRE" code="1#NOMBRE#longueur_message" />
        <item algoitem="clef EST_DU_TYPE CHAINE" code="1#CHAINE#clef" />
        <item algoitem="longueur_clef EST_DU_TYPE NOMBRE" code="1#NOMBRE#longueur_clef" />
        <item algoitem="i EST_DU_TYPE NOMBRE" code="1#NOMBRE#i" />
        <item algoitem="code_lettre EST_DU_TYPE NOMBRE" code="1#NOMBRE#code_lettre" />
        <item algoitem="decalage EST_DU_TYPE NOMBRE" code="1#NOMBRE#decalage" />
        <item algoitem="lettre EST_DU_TYPE CHAINE" code="1#CHAINE#lettre" />
    </item>
    <item algoitem="DEBUT_ALGORITHME" code="101#debutalgo" >
        <item algoitem="LIRE message" code="2#message#pasliste" />
        <item algoitem="LIRE clef" code="2#clef#pasliste" />
        <item algoitem="longueur_message PREND_LA_VALEUR message.length" code="5#longueur_message#message.length#pasliste" />
        <item algoitem="longueur_clef PREND_LA_VALEUR clef.length" code="5#longueur_clef#clef.length#pasliste" />
        <item algoitem="POUR i ALLANT_DE 1 A longueur_message" code="12#i#1#longueur_message" >
            <item algoitem="DEBUT_POUR" code="13#debutpour" />
            <item algoitem="code_lettre PREND_LA_VALEUR message.charCodeAt(i-1)-65" code="5#code_lettre#message.charCodeAt(i-1)-65#pasliste" />
            <item algoitem="decalage PREND_LA_VALEUR clef.charCodeAt((i-1)%longueur_clef)-65" code="5#decalage#clef.charCodeAt((i-1)%longueur_clef)-65#pasliste" />
            <item algoitem="lettre PREND_LA_VALEUR String.fromCharCode(65+(code_lettre+decalage)%26)" code="5#lettre#String.fromCharCode(65+(code_lettre+decalage)%26)#pasliste" />
            <item algoitem="AFFICHER lettre" code="3#lettre#0#pasliste" />
            <item algoitem="FIN_POUR" code="14#finpour" />
        </item>
    </item>
    <item algoitem="FIN_ALGORITHME" code="102#finalgo" />
</Algo>

 

Le cryptage affine, on peut utiliser le site :

Pour vous aider, vous pouvez utiliser le lien suivant qui permet de faire l'analyse fréquentielle d'un texte simple : Fréquence des lettres d’un texte ou directement l’adresse http://www.cryptage.org/outil-crypto-frequences.html

 

 

Utilisation de Verifinger :

Vous pouvez télécharger une démonstration de verifinger à l'adresse suivante:

http://www.neurotechnology.com/download/Neurotec_Biometric_4_0_Algorithm_Demo_2011-01-25.zip

 

Elle intègre :

Fingerprint identification algorithm demo;

Face identification algorithm demo;

Iris identification algorithm demo.

 

Base de donnée d'empreintes :

http://www.neurotechnology.com/download/CrossMatch_Sample_DB.zip

http://www.neurotechnology.com/download/UareU_sample_DB.zip

Neurotec_Biometric_4_0_Algorithm_Demo/Bin/Win32_x86/FingersAlgorithmDemo.exe

 

Après exécution du programme:

choisir une des options: identify (fast) , identify (full) ou Verify

p { margin-bottom: 0.21cm; }

Vous chargerez la base de donnée d'empreintes ( Open directory ):

 

p { margin-bottom: 0.21cm; }

Verifinger fait une analyse de chaque image de la base , en recherchant les minuties.Ce qui permettra une analyse rapide de l'image du suspect par la suite.

p { margin-bottom: 0.21cm; }

Vous pouvez ensuite charger l'empreinte du suspect ( Open file ...):

bouton droit de la souris pour le popmenu

p { margin-bottom: 0.21cm; }

On peut montrer les limites, on peut prendre une portion d’empreinte:

p { margin-bottom: 0.21cm; }

Ici,il ne trouve rien, car il y a un mauvais paramétrage du logiciel.

 

 

Il faut modifier le nombre de minuties dans le menu Tools pour obtenir un résultat . Il faut choisir le menu Tools -> options et modifier le nombre de minuties

 

Si,on fait l’essai avec une autre portion d’empreinte, il ne trouve rien, il faut donc modifier number of templates

Dans menu Tools mettre number of templates à 6 …

 

p { margin-bottom: 0.21cm; }

On peut choisir identify full ( cela donne le score de comparaison avec chaque empreinte de la base )

En réglant différents paramètres dans Tools -> options

 

p { margin-bottom: 0.21cm; }

Il trouve des correspondances même avec une petite portion d'empreinte.

 

 

p { margin-bottom: 0.21cm; }

On peut utiliser efinger, mais il ne permet de comparer que deux images à la fois.

Vous pourrez utiliser :
FacesAlgorithmDemo.exe pour la reconnaissance faciale
IrisesAlgorithmDemo.exe pour la reconnaissance rétinienne

 

p { margin-bottom: 0.21cm; }

Prise d'une empreinte sur un support non poreux :

p { margin-bottom: 0.21cm; }

On verse quelques gouttes de GLUE au fond du pot de verre et on ferme.

On peut placer dans un chauffe ballon ou sur un radiateur 5 à 10 minutes :

p { margin-bottom: 0.21cm; }

Le résultat : une empreinte bien visible.

 

On peut prendre ses empreintes sur du papier blanc à l'aide : d' un crayon de papier 2HB ou 2B , de l'encre de chine, du fond de teint liquide ou du mascara et ensuite scanner la feuille pour ensuite utiliser verifinger.

Par  C.R

Lycée Louis Lapicque

Epinal 88000

 

 

 

 

 

RASMOL

http://www.openrasmol.org/

RasTop

http://www.inrp.fr/Acces/biotic/rastop/accueil.htm

DS Visualizer

http://accelrys.com/products/discovery-studio/visualization-download.php

ICM-Browser

ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.

http://www.molsoft.com/getbrowser.cgi

ActiveICM 1.1.4

http://www.molsoft.com/activeicm.html

http://www.molsoft.com/getbrowser.cgi?product=activeicm&act=list

http://www.molsoft.com/getbrowser.cgi?product=activeicm&act=list

VMD 1.8.7

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

CN3D 4.1

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

Below is a relatively simple sample of what Cn3D can do. There are many more examples in the Tutorial, along with instructions to help new users get started!

This example is a curated CD of the WD40 domain, which is a multi-functional 7-fold beta propeller. Cn3D is showing a representative protein structure, the family alignment, and annotation panels with information about annotated features of this protein family. Highlighted in both structure and sequence windows are the conserved residues in a pattern characteristic to this domain.

 

WPDB 2.2

WPDB - The Protein Data Bank Through Microsoft Windows

http://www.sdsc.edu/pb/wpdb/wpdb.htm#Availability

Par ftp : ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/

 

DTMM 4.2 version Demo

http://www.polyhedron.co.uk/dtmmform

Desktop Molecular Modeller (DTMM)  is a simple-to-use molecular modelling program that enables you to perform powerful molecular synthesis, editing, energy minimizations, and display. The package, substantially enhanced from previous versions of DTMM, will run on any PC with Windows 95, 98, Me, 2000, NT, or XP.

gopenmol 3.0

g0penMol :

http://www.csc.fi/english/pages/g0penMol/Downloads/gopenmol-3.00-win32.zip

gOpenMol has its background in the SCARECROW program, which was introduced at the beginning of the 90s. In the middle of the 90s prof. Geerd Diercksen asked for a graphical interface for his OpenMol set of programs. This triggered off the development of gOpenMol. Since those days, the development of the program has been active, and today we can proudly present the updated version of the gOpenMol program. The current version is 3.00 released on 23.9.2005.

With gOpenMol small molecules, and to lesser extent protein structures, as well as the chemical properties, total electron densities and molecule orbitals of small molecules can be visualized and analyzed. Data from a variety of computational chemistry programs such as TurboMole, Gaussian, Gamess, etc., can be analyzed if the output files from these programs have been converted into the .plt-file format understood by gOpenMol. Moreover, dynamics done with, e.g., InsightII can be visualized and a short mpeg animation of the dynamics files generated.

On these pages you will find information about the program, the software and the development. These pages are also intended to improve the communication in the gOpenMol community.

 

POV-Ray 3.7b38

http://www.povray.org/

Mol2Mol 5.6.1 Demo

Molecule file manipulation and conversion program

for the Windows platform

version 5.6.2

What is Mol2Mol?

More than a decade ago, at the end of the 80's, the different molecular modelling programs have started widely to spread. These programs use different file formats to hold the coordinate and atomic data, and each formats follows unique syntax rules, which prevents the direct transfer of the molecules between the different applications. It was a serious drawback of the early programs, but even today there is a need for the transformation of molecule files. This led to the development of the original Mol2Mol several years ago.

The current version of Mol2Mol™ recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Problematic files can be corrected within Mol2mol or as ASCII files by calling directly your favourite text editor.

Mol2Mol is more than just a simple conversion system

It has a number of useful utilities:

• Calculation of basic geometrical data: distances, angles, dihedral angles;
• Calculation of atom pyramidalities, angle of rings, distances from least square planes, ring puckerings;
• Changing of bond types, atom types;
• Add or delete hydrogens, structural waters;
• Add hydrogens in pH dependent mode;
• Slicing of biopolymers or multiple files to individual molecules;
• Batch or many-to-many conversion;
• Merging of individual simple files to multiple ones;
• Browsing multiple files;
• Conversion of multiple structural files;
• Conversion of proteins to "backbone molecules", Ramachandran plot;
• Checking of peptide backbone geometry, adding CH₃, CH₂ centroid pseudo atoms;
• Manual editing of problematic files... and many others.

 

MolPOV 2.0.8

http://www.chem.ufl.edu/~der/der_pov2.htm

http://www.chem.ufl.edu/~der/MP2install.exe

PovChem 2.1.1

http://www.chemicalgraphics.com/PovChem/

What is PovChem? It's 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 for journal covers, advertisements, posters, anything!

Version 2.1 is now available for Macintosh! See the download page for more information.

I'm still actively in the process of updating PovChem with new features. And I need your help! Please Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. what functionality you'd like to see added in the near future, and in particular what features you feel you'd need to have before you'd consider purchasing a license. Things I'm considering for the near future are selection of atoms/bonds to adjust colors and radii, output of different 3-D formats like DXF or 3DS, ability to read in multiple PDB models, placement of backdrop or floor planes for shadows, etc. But I need to know what you as the user think is most important! So Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. , even just a brief one-liner, to help steer me in the right direction.

 

Ortep-3 2.02 http://www.chem.gla.ac.uk/~louis/software/ortep3/

Ortep-3 for Windows is a MS-Windows version of the current release of ORTEP-III (1.0.3), which incorporates a Graphical User Interface (GUI) to make production of thermal ellipsoid plots much easier. Most of the commonly used features of ORTEP-III are directly available from the GUI. Loading a coordinate file will result in a default view of the molecule immediately, and no knowledge of the inner workings of ORTEP is required to produce excellent publication quality output.

The main features of Ortep-3 for Windows are:

• Ortep-3 for Windows can directly read many of the common ASCII crystallographic file formats which hold information on the anisotropic displacement parameters. Currently supported formats are SHELX, GX, CIF, SPF, CRYSTALS, CSSR-XR, CSD-FDAT, GSAS, Sybyl MOL, XYZ, PDB, Rietica-(LHPM) and Fullprof.
• Ortep-3 for Windows will also read any legal ORTEP-III instruction file.
• Up to 999 atoms may be present in the asymmetric unit. Covalent radii for the first 94 elements are stored internally, and may be modified by the user.
• Several style-templates are supplied, but the graphical representations of thermal ellipsoids for any specific atom, or the bonds between any specified pairs of atoms can be individually chosen. Over 120 different colours are stored internally and up to 200 colours may be defined. All graphical objects may be drawn in any colour.
• The viewpoint can be rotated by dragging the left mouse button, in the standard Windows fashion.
• A mouse labelling routine is provided by the GUI. Any number of selected atoms may be labelled, and any available Windows font may be used for the labels.
• Graphic output in the following formats is supported : HPGL and PostScript, BMP. Direct printing to an on-line printer is also supported. It is also possible to prepare drawings of the correct size for direct reproduction in journals (many leading journals are now requesting this).
• Ray-traced output is available using the Raster3D or POV-Ray formats. Several representations are available from the POV-Ray interface, including thermal ellipsoids (standard ORTEP, RMSD and MSD surfaces) and van der Waals plots.
• A simple text-editor is provided, so that input files may be modified without leaving the program.
• Symmetry expansion of the asymmetric unit to give complete connected molecules may be carried out easily.
• Automatic unit cell packing diagrams.

 

PWT(PLATON for Windows Taskbar) 1.15

PLATON for MS-Windows : http://www.chem.gla.ac.uk/~louis/software/platon/

 

Current versions of the program PLATON for Windows are available from this site. The source code and compiled versions of the program for various other UNIX platforms are available from the official PLATON ftp-site. A full manual for PLATON is available from the PLATON homepage

PLATON is written by Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. , and is a versatile crystallographic tool implementing a large variety of standard geometrical calculations (i.e. bonds, angles, torsions, planes, rings, inter-molecular contacts (H-Bond analysis), Coordination etc), tests (i.e. for missing symmetry, voids in the lattice etc.), utilities (cell transformation, SHELXL input etc.), graphics (e.g automatic labelled 'ORTEP-lookalike plots and the molecular graphics program PLUTON) and several filters (e.g. the DIFABS technique for empirical absorption correction (Walker & Stuart), and the SQUEEZE option for handling disordered solvents, described by Sluis & Spek, Acta Cryst. 1990,A46, 194). This latter option places great demands on the available memory.

Parameter data may be given in various formats including CSD-FDAT, CIF, PDB & SHELX RES standards. A CIF file should be used when e.s.d.'s on the derived geometry parameters are desired. Most features are currently available only for non-protein structures.

 

Mage 6.44

http://kinemage.biochem.duke.edu/software/mage.php

Mage

http://kinemage.biochem.duke.edu/software/mage.php

Mage is a 3D vector display program which shows "kinemage" graphics. Used in both teaching and research, in applications ranging from estuary ecology to X-ray crystallography model quality assessments, Mage displays the 3D relationships between data in an interactive environment which facilitates both open-ended exploration and structured presentation. It includes many tools for on-screen measurement, construction, and editing of the display objects; it can write either kinemage output or various types of 2D image output.

Mage is available for several popular platforms. Pre-compiled executables or source code are available from the table below. To download: click the “Mage” name for the appropriate table-row.

The windows download is as the exe (not compressed, or otherwise protected), because we still encounter some Windows systems without a default compression/archival utility such as WinZIP. If you intend to use Mage's updating of contact-dots, you'll also need the Prekin and Probe programs. See our installation and use instructions for more detail. Further explanation of Windows-related use and installation is given in these notes from last semester.

 

Prekin 6.42

http://kinemage.biochem.duke.edu/downloads/software/prekin/

 

KiNG 2.17

KiNG

KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research. KiNG builds on Mage, JavaMage, and the "kinemage" (kinetic image) concept to deliver a full-featured Java application with a user-friendly interface and integrated editing features. The KiNG jar file can be used within a web page as a Java applet or Java object to promote easy access to kinemages or coordinate files from a web browser. Download kingInBrowser.zip for further instructions.

Versions of KiNG 2 and higher need a Java Virtual Machine of version 1.5 or higher. For MacOSX users, system version 10.4 or higher is needed. (KiNG version 1.6, which requires JVM 1.3 or higher, is available in our browsable download section.) For your convenience, we provide platform-specific installers that bundle a private copy of the Java runtime and libraries with the KiNG program itself. This installation of Java is used only by KiNG and will not cause conflicts with any other Java applications that may reside on your computer.

The Windows 2.14+ version of KiNG now includes Java 1.6, for better compatibility with Windows Vista Aero. If you downloaded an older version of KiNG previously, you will have to replace your download with a new version from the link below to get the new Java. Email vbc3 AT duke.edu if you have issues with the new version.

 

Swiss-PdbViewer 4.01

http://spdbv.vital-it.ch/

Swiss-PdbViewer DeepView v4.0

presents

by Nicolas Guex , Alexandre Diemand , Manuel C. Peitsch , & Torsten Schwede

 

News: version 4.0.1 has been released on October 7th 2008

• The Thymine C6 atom is now correctly loaded
• Fixed the POV-Ray output endless loop on the PC version
• The occasional crash while saving PDB files (such as 2i37) on the PC has been fixed
• Updated the address of the Uppsala Electron Density Map Server

Thank you to all users who reported those bugs!

 

News: version 4.0 has been released on June 27th 2008

• First of all, and most importantly, PC and Mac versions have been resynchronized.
• Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace
• Enhanced Import Menu
• Enhanced user interface with taxonomy support, and new sequence alignment features.
• New 3D Motif Searching feature
• Easy access to external user defined scripts directly from the interface
• Revised Help files accessible from the interface

 

Description

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze 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.

Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.

Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.

StrukEd Demo

http://www.struked.de/cgi-bin/dynapages.cgi?page=download_demo.html

JMVC 4 041122

http://www.adcworks.com/java3d-molecular-visualisation-system/

Re_View 1.0

http://server.ccl.net/cca/software/MS-WIN3/RE_VIEW-Demo/README.shtml

Oscail X

http://www.nuigalway.ie/cryst/software.html

Moilin X

http://www.nuigalway.ie/cryst/moilin.html

Tinker 5.1

http://dasher.wustl.edu/tinker/

http://dasher.wustl.edu/tinker/downloads/tinker-5.1.09.zip

 

Biodesigner

http://www.pirx.com/biodesigner/index.shtml

http://www.pirx.com/biodesigner/download.html

MoluCAD 1.034 Demo

Qmol 4.01

http://www.dnastar.com/qmol/

http://www.dnastar.com/qmol/Qmol.zip

Protein Explorer 2.80

Chimera 1.41

http://www.cgl.ucsf.edu/chimera/

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. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR01081).

Feature Highlight

Molecular Graphics

• stick, ball-and-stick, CPK, ribbon, pipe-and-plank, and nucleotide display styles
• molecular surfaces
• highly intuitive rotation, translation, and scaling with the mouse
• Side View for adjusting clipping planes and scaling
• interactive color editing in various color spaces (RGB, CMYK, etc.) with transparency
• ability to save high-resolution images for presentation and publication
• stereo (side-by-side and time-sequential)

Jmol 12.0.12

http://jmol.sourceforge.net/index.fr.html

Ramachandran Plot Explorer 1.0

http://boscoh.com/ramaplot/

http://boscoh.com/ramaplot/rama-1.0-win.zip

http://boscoh.com/ramaplot/rama-1.0-osx.zip

ProteinScope LE 1.0.5

http://www.uplink.to/ProteinScope/

What is ProteinScope?

• A single, integrated application for your desktop
• Hand optimized 3D for complex molecules
• Use arrow keys to rotate molecule
• Full screen mode for 3D glasses
• Separate DNA / protein complexes
• Hydrophobicity and temperature color schemes
• Create Excel spreadsheets of all or part of a PDB

Create animations, slides and spreadsheets for:

• PowerPoint presentations of research and lectures
• Enhance grant proposals
• Include protein graphics on web sites
• Zoom into binding sites for snapshots
• Highlight sequence motifs
• Use Excel^* macros for data processing

 

CHIME 2.6 SP8

http://accelrys.com/products/informatics/cheminformatics/

 

YASARA View 9.11.22

http://www.yasara.org/

NOC 3.01

http://noch.sourceforge.net/

3DNA 1.5

http://rutchem.rutgers.edu/~xiangjun/3DNA/ (biologie )

ArgusLab 4.0.1

http://www.arguslab.com/

http://www.arguslab.com/ArgusLab40/arguslab.zip

 

ArgusLab
A molecular modeling, graphics, and drug design program

ArgusLab is freely licensed

Over 20,000 downloads and still growing!

CueMol 1.1.0.196

http://cuemol.sourceforge.jp/en/

http://prdownloads.sourceforge.net/cuemol/cuemol-1.1.0.196-setup.exe?download

CueMol is a program for the macromolecular structure visualization on the Windows platform (CueMol was formerly called "Que"). CueMol aims to visualize and build the crystallographic models of macromolecules, with the user-friendly interfaces. Currently supported files are molecular coordinates (PDB format), electron density (CCP4, CNS , and BRIX format), MSMS surface data, and GRASP electrostatic potential map.

 

 

jimp 2 0.091

http://www.chem.tamu.edu/jimp2/predownload.html

Jimp 2 is a free program for visualizing and manipulating molecules. It is being written by Josiah Manson and Charles Edwin Webster under the supervision of Dr. Michael Hall and is funded by the Texas A&M Department of Chemistry and the National Science Foundation under grants: CHE-9800184, CHE-0518078, and CHE-0541587. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

All publications and/or presentations that result from the use of Jimp 2 should contain the following references: Hall, M. B.; Fenske, R. F. Inorg. Chem. 1972, 11, 768-779. Manson, J.; Webster, C. E.; Pérez, L. M.; Hall, M. B. http://www.chem.tamu.edu/jimp2/index.html

Programming of Jimp 2 was started in the Summer of 2004 and has been under development throughout the Summer of 2005. We now believe that Jimp 2 has reached a stable form and can be unleashed upon the masses.

Since its predecessor, Jimp 2 was started completely fresh. One of the most basic changes that users will notice is that Jimp 2 has its data organized in a hierarchical tree structure, compared to the layer structure of Jimp. Internally, there are several major changes; one of the bigger changes is that everything is driven by a scripting language (written by one of the authors, Josiah Manson). Scripting allows for tedious tasks to be automated. As well, every action done through the GUI is executed through the scripting language and logged, so it is easy to generate macros and to learn how the scripting works.

 

SweetMollyGrace 1.3

http://rodomontano.altervista.org/engSweetMG.php

http://rodomontano.altervista.org/downloads.php?download=http://rodomontano.altervista.org/fclick/fclick.php?fid=107

Facio 14.3.1

http://www1.bbiq.jp/zzzfelis/Facio.html

http://www1.bbiq.jp/zzzfelis/software/Facio1432.zip

VEGA ZZ 2.3.2

http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ

VEGA ZZ Molecular Modeling Toolkit

http://www.ddl.unimi.it/vega/packages/Vega_ZZ_2.4.0_Hybrid_Setup.exe

VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.

GDIS 0.90

http://gdis.sourceforge.net/

http://gdis.sourceforge.net/download.html

GDIS is a scientific visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures. It is in development, but is nonetheless quite functional. It has the following features:

• Support for many common file formats (CIF, PDB, XTL, XYZ, and many more).
• Job submission tools for computational chemistry packages: GAMESS, GULP, ReaxMD, and SIESTA.
• Job analysis and graphing tools for dynamics simulations.
• Useful manipulation tools, including matrix transformations and supercell construction.
• Powerful surface generation and crystal morphology tools.
• Diffraction pattern generation and plotting.
• Animation of multi-frame files.
• Assorted tools for visualization (measurements, ribbons, polyhedral display).

QuteMol

http://sourceforge.net/project/showfiles.php?group_id=169766

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

• Real Time Ambient Occlusion
• Depth Aware Silhouette Enhancement
• Ball and Sticks, Space-Fill and Liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web pages animations
• Real-time rendering of large molecules and protein (>100k atoms)
• Standard PDB input
• Quick installers for Win and Mac OS X (intel) (new!)
• Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-composites

QuteMol was developed by Marco Tarini and Paolo Cignoni of the Visual Computing Lab at  ISTI - CNR

 

Ascalaph 1.7.7

http://www.biomolecular-modeling.com/Products.html

http://www.biomolecular-modeling.com/Purchase.html

Abalone is designed for macromolecular simulations (proteins, DNA). It supports both explicit and implicit solvent models. In contrast to Ascalaph, tailored to the simulation of small molecules, Abalone is focused on molecular dynamics modeling of biopolymers. It supports such effective methods as the Replica Exchange and hybrid Monte Carlo. Abalone is easy to install and it requires no external programs.

BALLView 2.0-r1

http://www.ballview.org/

BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS.

Important Note (Update):

A raytracing version for windows has been released and is ready for download. Just head to the Downloads section, or explore some screenshots at the raytracing gallery

 

BioEditor & BioViewer

http://bioeditor.sdsc.edu/index.shtml

http://bioeditor.sdsc.edu/download.shtml

http://bioeditor.sdsc.edu/download.shtml

Overview: Once a macromolecular structure has been determined, the challenge is to communicate that information to a widely diverse audience of scientists, educators and students. Current options include the printed literature and dissemination over the Internet, either via online journals or directly on personal web pages. Printed literature has the advantage of wide acceptance and availability, but presents static images. Web pages can be powerful, but lack a uniform format. Furthermore, any dynamic images that are presented are subject to the whims of the providers of the browsers and plug-ins that are required to view them. At the University of California, San Diego and the Scripps Institute, we are developing the BioEditor as a tool to bridge the gap between the printed literature and current Internet presentation formats. It is a standalone Windows application that can be used to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. This presentation will summarize the features of BioEditor and provide an overview of a series of annotations that have been developed on DNA-protein complexes.

ProteinShader beta 0.9.4

http://proteinshader.sourceforge.net/

PDB Editor 090203

http://sourceforge.net/projects/pdbeditorjl/

Zodiac 0.65

http://www.zeden.org/

Avogadro 1.0.1

http://avogadro.openmolecules.net/wiki/Avogadro_1.0.1

http://avogadro.openmolecules.net/wiki/Get_Avogadro

Bioclipse 2.4.0

http://www.bioclipse.net/

http://www.bioclipse.net/download

Bioclipse is a free and open source workbench for the life sciences.

Bioclipse is based on the Eclipse Rich Client Platform (RCP) which means that Bioclipse inherits a state-of-the-art plugin architecture, functionality, and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

 

Antheprot 3D

http://antheprot-pbil.ibcp.fr/

Chemis3D 2.72

http://chemis.free.fr/mol3d/

Chemis3D, Molecular Viewer Applet

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document.
It is specially designed for open interactive molecular visualization on the Internet or via an intranet.

 

Chemitorium 3.0

http://weltweitimnetz.de/chemitorium_en.htm

http://weltweitimnetz.de/files/chemitorium_inst.exe

LigandScout 3.01

http://www.inteligand.com/ligandscout/

LigandScout 3.0

LigandScout 3.0 is a fully integrated platform for accurate virtual screening based on 3D chemical feature pharmacophore models. It offers seamless workflows, starting both from ligand- and structure based pharmacophore modeling, and includes novel high performance alignment algorithms for excellent prediction quality with unprecedented screening speed. Additionally, we have included user-friendly screening analysis tools, including the automated generation of ROC curves for performance assessments. All functions are accessible through a well elaborated graphic user interface that reflects our years of experience in creation of the most user-friendly pharmacophore modeling tools. The algorithms are scientifically validated and based on our well-established knowledge in pharmacophore research, while the application corresponds to state-of-the-art information technology.

The algorithms are scientifically published [1-4] and based on several years of experience in pharmacophore creation, while the application corresponds to state-of-the-art information technology. Support for various common pharmacophore formats like the export to Catalyst^tm, MOE^tm or Phase^tm guarantee maximum interoperability to screening platforms. The full-featured 3D graphical user interface with multiple undo-levels makes the exploration of the active site and pharmacophore creation within the complex efficient and transparent. Binding site analysis, pharmacophore-based alignment and the creation of shared feature pharmacophores are designed to make LigandScout an essential tool for structure-based drug design in combination with virtual screening. LigandScout runs on all common operating systems.

Free evaluation: You can download a fully functional version and test it for one month by registering. For longer or scheduled evaluation periods, further information or scientific questions contact Gerhard Wolber ( Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. ).

 

AutoDock 4.2.3

http://autodock.scripps.edu/

http://autodock.scripps.edu/downloads

utoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids.

In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.

We have also developed a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.

AutoDock has applications in:

• X-ray crystallography;
• structure-based drug design;
• lead optimization;
• virtual screening (HTS);
• combinatorial library design;
• protein-protein docking;
• chemical mechanism studies.

AutoDock 4 is free and is available under the GNU General Public License. Click on the "Downloads" tab. And Happy Docking!

 

PyRx

http://sourceforge.net/projects/pyrx/

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening form any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design.Visit Videos page for Getting Started Screencasts. See also Starting Virtual Screening and Getting Started with PyRx tutorials.

PyRx is using large body of established open source software such as:

· AutoDock 4 and AutoDock Vina are used as a docking software.

· AutoDockTools, used to generate input files.

· Python as a programming/scripting language.

· wxPython for cross-platform GUI.

· The Visualization ToolKit (VTK) by Kitware, Inc.

· Enthought Tool Suite, including Traits, for application building blocks.

· Opal Toolkit for running AutoDock remotely using web services.

· Open Babel for importing SDF files, removing salts and energy minimization.

· matplotlib for 2D plotting.

 

VisProt3DS 2.0

http://www.molsystems.com/vp3ds.html

Look at the Proteins and DNA in 3D stereoscopic view by anaglyph or side by side mode (or with shutter glasses). Using VisProt3DS some people can see stereo without any glasses by side by side mode at least in small window. Any person with binocular sight can see 3D Stereo image of complex proteins on full screen using simple and the cheapest anaglyph technology (color separated). VisProt3DS is the program for protein and DNA visualization from PDB (Protein Data Bank). It may be also called protein visualizer or protein viewer. The program have simple interface to manipulate proteins and DNA for scientific goals, education purposes with curiosity or simply for a fun.

OpenAstexViewer 3.0

http://openastexviewer.net/web/ Software for molecular visualisation.

Developed by Mike Hartshorn whilst at Astex Therapeutics Ltd.

COSMOS Viewer 3.0

http://www.cosmos-software.de/cosview_e.html

MOIL

http://cbsu.tc.cornell.edu/software/moil/moil.html

We announce the release of a new version of the package for molecular dynamics and modeling MOIL¹ -  MOIL11. The complete source code is included. Ready execution files are available for Windows XP, Mac OS/X, and Linux (Fedora). The code is in the public domain. You may use it or any portion of it in any way you like. The only requirement is that references will be made to the original authors in any study that uses MOIL. New codes that build on MOIL should detail the extent of use and include in their release notes the first paragraph of this message.

 

Moil supports the usual set of tools for molecular modeling by classical mechanics, including energy calculations, energy minimization, molecular dynamics, and more. Code is available to simulate curve crossing within the Landau Zener model. Moil allows for reasonably straightforward conversion of PDB files to computable datasets (coordinate and energy templates).

 

Besides “standard” applications MOIL evolves around the research in Ron Elber’s laboratory. Examples are the Locally Enhanced Sampling Approach² and reaction path and long time dynamics algorithms ³ that are based on action optimization. Also included the recently developed Milestoning approach for the calculation of kinetics and thermodynamics along a reaction coordinate⁴. The integration of a coarse-grained model into moil is yet another new feature of MOIL11.

 

Numerous examples and templates are included in the moil/moil.test directory. Documentations are in moil/moil.doc. A dictionary of keywords used in moil is available at moil/moil.doc/dictionary.txt

 

Significant new enhancements to the older version(s) include

1. Get a pre built code http://clsb.ices.utexas.edu/prebuilt or signed on a SVN server for continuous updates of source code https://wiki.ices.utexas.edu/clsb/wiki
2. A new visualization program (zmoil) for graphic display of individual structures, dynamics, reaction paths and overlay of multiple structures, read PDB CRD DCD and (MOIL specific) PTH formatted files. (by Thomas Blom and Baohua Wang)
3. Enhanced graphic interface moil.tcl for numerical simulations with numerous bug fixes. Not all moil modules are supported by the graphic interface  (by Thomas Blom and Baohua Wang)
4. A new coarse-grained model of proteins (two points per amino acid) for energy, minimization, dynamics and path calculations (by Peter Majek)
5. Replica exchange (by Serdal Kirmizialtin)
6. New code for stochastic optimization of  approximate trajectories with large step (SDEL by Peter Majek)
7. Steepest descent path calculation by action optimization (sdp module by Ron Elber and Peter Majek)
8. Milestoning simulations of kinetics (the fp module by Anthony West)
9. Implementation of OPLS DNA/RNA force field in addition to OPLS for proteins and liquid simulations (by Serdal Kirmizialtin)
10. Calculation of pressure (by Luca Maragliano)

 

MOIL11 team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron Elber

 

MMV 2.0.0

http://www.molegro.com/mmv-product.php

Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and Molegro Virtual Docker results.

Molegro Molecular Viewer is able to visualize most common molecular file formats (PDB, Mol2, SDF) as well as docking results from Molegro Virtual Docker.The latest version of MMV is 2.1.0 (released October 15th, 2010).

Features at a glance

• Free!
• Cross-platform: Windows, Linux, and Mac OS X is supported.
• Share and view results from Molegro Virtual Docker docking runs.
• Imports and exports PDB, SDF, Mol2, and MVDML files.
• Built-in raytracer for high-quality images.
• Automatic preparation of molecules.
• Molecular surface and backbone visualization.
• Labels, sequence viewer and biomolecule generator.
• Cropping of molecules and clipping planes.
• Structural protein alignment.

 

OpenMM 2.0

https://simtk.org/home/openmm

https://simtk.org/frs/download.php?file_id=2378

Description: OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding.

Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.

 

Chemsketch

http://www.acdlabs.com/resources/freeware/chemsketch/

 

DINO

http://www.dino3d.org/

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i586 and Mac OSX. Versions for IRIX, OSF1 and SunOS are made available sporadically, usually upon request.

 

Ascalaph Graphics

http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html

Ascalaph Graphics is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix.
http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html
# Molecular graphics
Multiple windows
Two cameras per model
CPK, Wire frame, Stick, Ball and Stick and CPK Wire frame styles

# Molecular model building

Chain Builder
Crystal builder
Geometry editing

# Molecular dynamics
Multiple time step integration
Calculations on clusters with aid of MDynaMix
Flexible SPC water model

Draw molecule with a mouse