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  • Software per l' apprendimento

    RasMol Home Page

    Molecular Visualization Freeware for proteins, dna and macromolecules.

    Wavefunction, Inc.

    With Spartan in the classroom you can visualize what before was incomprehensible. In the laboratory, you can explore novel drug candidates. With the right tools there are no limits. Spartan combines state-of-the-art visualization with powerful calculations in a complete but affordable and remarkably easy-to-use molecular modeling package. Supporting Windows, Macintosh, Unix and Linux, Wavefunction provides solutions for chemists in industry and academia.

    JChemPaint

    JChemPaint [KRA00] is an editor for 2D Molecular Structures, like this one here . JChemPaint is intended to be complementary to JMol, a visualisation and analysis tool for 3D molecular structures, started by Dan Gezelter at Notre Dame University , initator of the Open Science Project. and, like JChemPaint, developed by an international team of open-source programmers.

    UCI Chemistry

    Here are some Java applets that give you a chance to explore some scientific principles the same way a professional scientist does: by messing around with a system that exhibits the principle. The main difference is that these systems are all simulated -- they exist only on your computer. But they are quite realistic, in the sense that their properties are calculated carefully by accurate and modern scientific methods. Indeed, simulations such as these form an important modern scientific research tool.

    Chem-It

    Chem-It offers everything the Chemistry student needs to work efficiently. The program performs common conversions automatically. There are reference areas which contain commonly used constants. The interactive periodic table houses all information a student might need about each element. The mass calculator allows you to calculate the mass of very complex substances using simple menus. During experiments, there is a built-in timer which makes it easy to time reactions. Additionally, there is a built in text editor which allows you to type your experiment notes without leaving the program.

    ACD/Free Stuff

    FREE DOWNLOAD PAGE: NMR software, spectra viewers, chemical drawing and modelling software, on-line service (ILAB), documentation, demo movies, screensaver

    Scientific Applications on Linux

    SAL (Scientific Applications on Linux) is a collection of information and links to software of interest to scientists and engineers.

    Software per Linux

    Questa pagina contiene dei link che fanno riferimento quasi esclusivamente al mondo della programmazione ed alla chimica, questi siti sono stati raccolti per fornire un utile elenco di siti in cui reperire del software che per lo più è free

    Welcome to GROMACS

    GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

    Chimicando.it

    Questa sezione la dedico a tutti i programmi inerenti la chimica e ad applicazioni utili allo svolgimento di determinati calcoli, spero di inserire oggetti interessanti e funzionanti. Anche in questo caso sono ben accetti i vostri contributi sia personali che non. Dimenticavo! I file sono stati controllati con la versione più recente del Norton Antivirus, ma la prudenza non è mai troppa. I software che sono disponibili questa pagina sono tutti gratuiti per uso privato e scolastico, ma dovrebbero essere comunque registrati. Visitate, cliccando sulle immagini, i siti delle rispettive società!!!!

    SOFTWARE DI CHIMICA

    1. ACDLabs 5.00 :ottimo software per creare qualsiasi molecola chimica, si può sapere il suo nome e vedere la sua struttura tridimensionale; compatibile con Microsoft® Word. Il migliore in questo campo. La versione è freeware. 2. ISIS Draw 2.4 : buon software per creare molecole e vederle in 3D, non vi dà il nome della molecola. La versione è freeware. 3. ChemLab 2.0 : ottimo software per simulare gli esperimenti in laboratorio, divertentissimo. La versione è freeware. 4. IR Tutor 1.1 : buon software per imparare che cos'è la spettroscopia e come leggere gli spettri IR. La versione è freeware.

    MDL Information Systems

    AutoNom Standard Add-in for ISIS/Draw and ISIS/Base: Automatic Nomenclature generates IUPAC chemical names directly from graphical structures created in ISIS/Draw or registered in ISIS/Base. MDL Chime: A chemical structure visualization plug-in for Internet Explorer and Netscape Communicator. Draw structures with ISIS/Draw and visualize them in 2D or 3D. MDL Custom Price Loading Tool: For licensed Reagent Selector and CPI customers only. MDL Data Analysis Toolbox: A biological curve fitting and data analysis tool. MDL ISIS/Draw: A chemically intelligent drawing package that enables you to draw chemical structures using the same intuitive signs and symbols used for paper sketches. FREE for academic and personal home use only. MDL CTFile Formats.

    CRYSTALLOGRAPHIC COMPUTER PROGRAMS

    The computer programs of the following list can be downloaded by clicking on the name of the program . The FORTRAN sources have the extention .FOR, while the compiled codes have the extentions: .EXE for PC/DOS, .sg for Silicon Graphics machines. The source codes can be compiled on every machine equipped with suitable FORTRAN77 compiler. To run these programs key in the name of the program with no extention if operating under DOS, with the extention .sg if on a Silicon Graphic machine. For all the programs the computer asks for the names of the input and output files that have to be keyed in by the user. More detailed instructions are given as comments at the heads of the source codes. The author will be glad to be informed by e-mail about the success (or the failure) of downloading and use of the programs.

    Alchimedia

    Sviluppo e realizzazione di software didattico-scientifico applicativi volti a risolvere problemi e semplificare procedure ipertesti per la diffusione della conoscenza scientifica e l'insegnamento software, materiale didattico, articoli di: chimica e ambiente, alimenti, ecc.

    ChemVis

    Chemical Visualization on the Internet.

    Computational Center for Macromolecular Structure.

    The Computational Center for Macromolecular Structure (CCMS) is distributing and supporting software for the determination and analysis of the structures of biological macromolecules. CCMS is a joint project of UCSD , The Scripps Research Institute , and the San Diego Supercomputer Center , supported by the National Science Foundation. Software is distributed and supported through the San Diego Supercomputer Center.

    Cn3D

    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!

    Chem3D

    CambridgeSoft Corporation, formerly Cambridge Scientific Computing, provides free demonstration versions of their commercial programs ChemDraw & Chem3D. They provide versions for Windows, MacIntosh, and unix. ChemDraw provides sophisticated drawing tools for 2D chemical structures. Chem3D displays molecules in 3D (optional stereo), with rotation and various representation options.

    Swiss-PdbViewer

    Swiss-PdbViewer 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. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB ) in collaboration between GlaxoSmithKline R&D and the Structural Bioinformatics Group at the Biozentrum in Basel.

    MOLMOL

    MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.

    MAGE

    MAGE can show different conformations of a molecule. For example, it can show the effect of substrate occupancy on the conformation of the active site of an enzyme. This "molecular animation" capability of MAGE is something which RasMol does not provide. Such conformational changes can, however, be toggled or morphed in Chime as pseudo-NMR files, or animated as XYZ files (see the animated thermal vibrations mapped to peaks in an infrared spectrum, for example).

    VMD

    VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

    ChemPen and ChemPen+ © Chemical Structure Drawing

    ChemPen is the the low cost, easy to use tool for chemists, educators and students who need to create create drawings for chemical documentation. ChemPen+ includes everything in ChemPen plus basic C-13 chemical shift prediction.Drawing with ChemPen is done with menus, mouse clicks and simple editors. Drawings can be pasted into Windows® graphics applications. ChemPen calculates molecular weight, molecular formula and elemental composition. Watch the animation below or click the drawing to see how easy it was created with ChemPen.

    COMSOL : FEMLAB - Multiphysics Modeling

    FEMLAB is an interactive environment for modeling and simulating scientific and engineering problems based on partial differential equations.

    The IrYdium Project

    The IrYdium Project would like to welcome you to a new paradigm for the use of computing in chemical education. Enjoy our current selection of applets.

    RasMol Program etc./UMass Amherst

    Protein Explorer, a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. And it's free! It runs on Windows or Macintosh/PPC computers. (linux users see below.) RasMol users will find its menus very familiar, and it understands RasMol commands. It is very fast: rotating a protein or DNA molecule shows its 3D structure. If you have never seen this, watch the image at the upper right of this page. (Click here to see another molecule rotate.) Look at our gallery to see still snapshots of other molecules.

    NET Engineering

    NET Engineering è un distributore a valore aggiunto di pacchetti software leader nel settore scientifico e business. Fondata nel 1996, NET Engineering nasce dall'esperienza maturata dai fondatori nel settore della progettazione, della ricerca e della analisi dei mercati. Attraverso costanti aggiornamenti, pubblicazioni e corsi, NET Engineering cerca di rispondere ai desideri ed agli interessi di ricercatori, scienziati e professionisti italiani e non. Il suo core-business è fornire soluzioni innovative di Information Technology con l'obiettivo di aiutare i clienti a semplificare il proprio lavoro e a incrementare il proprio business. Per ogni informazione, potete contattarci inviando una e-mail. Un saluto dal team.

    Applet

    Ecco alcune delle applet più popolari e divertenti di Physics 2000, fra cui alcune anteprime di applet che non sono ancora state inserite nelle pagine del sito.

    Windows Protein Data Bank, WPDB

    This program is offered free from the Computational Center for Macromolecular Structures (CCMS) of the San Diego Supercomputer Center. WPDB comes with a compressed PDB database of 320 proteins and nucleic acids chosen to represent unique structures, and a means to search for structures of interest. Version 2.0 was released in 1995, and comes zipped into a file larger than 6 megabytes. It provides limited viewing capabilities, and can use RasMol as a viewer for more sophisticated viewing. Its strengths include sequence alignment, structure superposition, secondary structure assignment, contact maps, and profiles of volume, hydrophobicity, polarity, isoelectric point, and mean exposure.

    Applet

    Ecco alcune delle applet più popolari e divertenti di Physics 2000, fra cui alcune anteprime di applet che non sono ancora state inserite nelle pagine del sito.

    Software per la Scienza e la Tecnica

    Il software per la chimica ha avuto negli ultimi anni un enorme sviluppo, in stretta correlazione con lo sviluppo dei sistemi operativi ad interfaccia grafica. Ora la modellazione molecolare, il disegno di strutture chimiche, e il referimento di informazioni chimiche, biologiche e genetiche non è più un problema. ChemBio3D Ultra 11.0 [Prodotto da: CambridgeSoft] Disegno di molecole, proteine e strutture in 3D ChemBioDraw Ultra 11.0 [Prodotto da: CambridgeSoft] Suite per il disegno di strutture chimiche e biologiche ChemBioOffice Ultra 2008 [Prodotto da: CambridgeSoft] Suite per la chimica e la biologia ChemDraw 11.0 [Prodotto da: CambridgeSoft] Disegno di strutture chimiche e meccanismi di reazione ChemFinder [Prodotto da: CambridgeSoft] Ricerca e integrazione di informazioni chimiche ChemOffice 2008 [Prodotto da: CambridgeSoft] Suite comprendente ChemDraw, Chem3d e ChemFinder E-Notebook Ultra 11.0 [Prodotto da: CambridgeSoft] Quaderno elettronico per ricercatori chimici Hyperchem 8.0 per Windows [Prodotto da: Hypercube,Inc.] Software per la modellazione di molecole Hyperchem for MAC [Prodotto da: Hypercube,Inc.] Modellazione di molecole Inventory Ultra 11.0 [Prodotto da: CambridgeSoft] Software per la gestione del reagentario Merck Index 14th Edition [Prodotto da: CambridgeSoft] Database per la ricerca di farmaci, composti chimici e biologici

    Rodomontano ChemDigit - Chemical Calculator

    Features ChemDigiT is a chemical calculator. No approximations made. All calculated variables show their exact values. The algorithm used for calculations is based on a full set of equations describing acid/base and salt dissociation equlibrium solved with Newton–Raphson method. * pH Acid-Base Section * Find exact pH and equilibrium concentrations of all dissociated and undissociated species of any solution of strong/weak/polyprotic acid and base. Built-in database of over 60 weak acids and bases with pka and pkb editable tables * pH Hydrolysis Section * Find exact pH and equilibrium concentrations of all dissociated and undissociated species of any solution of salt. * pH Mixtures Section * Find exact pH and equilibrium concentrations of all dissociated and undissociated species of any mixture of two acids or two bases * Titration Section * Trace titration curve and find pH and volume of titrant added at equivalent points of any combination of strong/weak acid-base * Balance Section * Balance chemical equations (max 8 reagents and 8 products). If Weight or mole of one specie is entered, amounts of all reagents and products will be calculated. If more than one value is entered, then ChemDigiT checks if there is a limiting reagent. If so this value is used for the stoichiometric calculation. * Concentration Section * Calculate and convert concentration (molarity, molality, percent concentrations and molar fractions). All calculations will automatically take solution density into account. Built-in editable database of over 300 compounds with density tables Calculator for dilution and solution mixing calculations. * Buffer Section * Calculate A) buffer composition (acid and conjugated base concentration) or B) desired pH and total concentration. ChemDigiT doesn't use Henderson-Hasselbach equation, but exactly solves a sixth degree equation. Ionic Strength option to consider activities. Davies equation parameters editable. Calculate new pH after addition of strong acid/base. * Solubility Section * Calculate solubility, pH and Ionic Strength of any solution of poorly soluble strong electrolyte. Built-in editable database of over 120 compounds with Solubility Product Constants. Evaluate effects of Hydrolysis (Anion), pH and Ionic Strength on the Solubility