	Inhaltsübersicht \| Nanomaschinen \| Moleküle \| Programme \| Kurse \| Fun \| Links
Kontakt \| Home	>

Links

Da die auf dieser Seite aufgelisteten Web Sites alle in englischer Sprache sind,
übernehme ich auch deren Beschreibung auf Englisch:

An excellent starting point in the search of anything related to molecular structure visualization is the World Index of Molecular Visualization Ressources by Eric Martz, listing Biochemical structure tutorials, Organic chemistry structure tutorials, Inorganic chemistry and crystal structure tutorials, Teaching tools, Non-English ressources, Tutorials on how to create Chime-based tutorial, Deep View/Swiss PDB viewer ressources, Sources of PDB files, Galleries of Molecular Images, E-mail Lists and Newsgroups on Molecular Visualization, Physical Models and Molecular Sculpture, Free Software for Molecular Modelling and Visualization and Commercial Software

Informationen über besonders interessante Moleküle

The PDB Molecule of the Month at RCSB by David S. Goodsell feature the structures of important biomolecules, focussing on the 3D-Structure and structure-function relationship
The InterPro Protein of the Month series at EMBL-EBI explores the function and family relationships of selected proteins from the InterPro database. PDB and InterPro collaborate, PDB focussing the 3D-structure, InterPro at sequence- and gene family relationships of the same protein
The Expasy Protein Spotlight at ExPASy is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics, describing a specific protein or family of proteins in an informal tone.
J. Chemistry Education Molecule of the Month
The Nucleic Acid Structure and Recognition web site (Oxford University Press) complements a book of the same name by Stephen Neidle and contains files that display molecules described in the book.
The Molecule of the Month at the University of Bristol offers a list of links to Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule. The (Occasional) Molecules of the Month at Imperial College, the Prous Science Molecule of the Month, The VCU Dept. of Medicinal Chemistry's Featured Drug Target, the Sciencegeek's Molecule of the Month (for the most recent one, you have to guess what it is)
3D Molecules of the Month at 3Dchem.com focusses on the 3D structure of small molecules, including some nice Jmol representations and a library of inorganic structures
J. Chemistry Education Molecule of the Month
Biomolecules at Kenyon Molecular Biology Tutorials by students from BIOL 263: Molecular Biology and Genomics (Chime and Jmol) and Molecules for Teaching (PDB files for download)
World of Molecules, Molecular Library
The Online Macromolecular Museum (some of the exhibits use Chime, others Jmol)
The DCU Molecular Viewing Gallery (small molecules)
The Atlas of Macromolecules at the University of Massachusetts is Eric Martz's collection of tutorials using the Protein Explorer (Chime). Visit also: MolViz.org
The Virtual Museum of Minerals and Molecules™ is a web-based focal point and resource for 3-D visualizations of molecules and minerals
BioMoleculesAlive is a digital library that provides an electronically accessible repository of high quality instructional materials and learning objects that can be used primarily by educators at the undergraduate, graduate and medical school levels to augment classroom, laboratory and independent learning.
The Coffee Break Tutorials for NCBI Tools teach how to search the different databases at NCBI (Literature, DNA and Protein Sequences, Taxonomic information and much more). NCBI also offers access to a number of online Textbooks
History of Visualization of Biological Macromolecules (On-line Museum)
The Anatomy and Taxonomy of Protein Structure (Jane S. Richardson)
Cells alive!
Biochemistry of Metabolism (info, index)
Molecules in Motion

Datenbanken

The RCSB Protein Database - An Information Portal to Biological Macromolecular Structures
The National Center for Biotechnology Information (NCBI) national resource for molecular biology information combines biomedical literature, DNA and protein sequences, taxonomic information and much more
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
The Nucleic Acid Database - A repository of three-dimensional structural information about nucleic acids
The Cambridge Structural Database - The world repository of small molecule crystal structures
The Inorganic Crystal Structure Database (ICSD) - the world's most extensive numeric database of inorganic crystal structure data
The Database of Macromolecular Movements and Morph Server with Associated Tools for Flexibility and Geometric Analysis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
CATH Protein Structure Classification Database (UCL)
Ligand-Depot
Klotho: Biochemical Compounds Declarative Database (Klotho: Alphabetical Compound List)
Atlas of Protein Side-Chain Interactions
InterPro: Home
Protein Kinase Ressource
MutaProt Comparison of PDB files which differ by point mutations
HiC-Up Hetero-compound Information Centre - Uppsala

Chemische Formelzeichenprogramme

JChemPaint is an open-source, java-based editor for 2D molecular structures, intended to be complementary to Jmol. It is avalable both as stand-alone program and as web viewer and editor applet
ACD ChemSketch is a restricted freeware version of a more extensive commercial software (Windows only)
The ACD Structure Drawing Applet is a java-based Web editor for 2D molecular structures.
IsisDraw is a Plug-In for the Microsoft Explorer (Windows only)

3D-Visualisierung

Pure molecular vizualization programs allow the interactive visualization of 3D-structure in various representation. They do not allow to edit the structure of the molecule.

Index of Free Molecular Visualization and Modeling Software

Jmol Homepage (Open source java application and web applet)

Documentation,
Jmol Demonstration Pages and most recent beta test versions
regular Download
JavaScript Library
Jmol Wiki
WebsitesUsingJmol
First Glance A simple, Jmol-based tool for macromolecular visualization
Convert CHIME to Jmol
Jmol_Web_Page_Maker

Rasmol classical 3D molecule viewer application; Chime and Jmol are derived from Rasmol, the three share the same script language

Chime Webbrowser plugin, no longer supported under MacOSX and Linux

MDL® Chime
MDL Information Systems :: Support :: Knowledge Base :: FAQs ::
Chime Tutorial
Chime Tutorial Visualization Tools
Chime Tutorial Obtaining Coordinates
Protein Explorer is a chime-based free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers. (Purpose of Protein Explorer)
Protein Morpher
MolSlides are annotated slides of rotating 3D views molecular structure. They are created with Protein Explorer (PE)

Pymol Cross-platform molecular visualization program with extensive scripting capabilities through its integration of the Python programming language. Allows limited conformational editing and recombination of coordinate files.

UCSF Chimera

Cn3D - structure and sequence alignment viewer for NCBI databases

Mercury - Crystal Structure Visualisation and Exploration Made Easy (Viewer for Cambridge Structural Database)

Kinemage Homepage

The Protein Chemist's Toolkit

Molekülmodellierung

Molecular modelling programs not only allow to visualize existing structures, but also to build structure models, analyze and energy-minimize these models.

Swiss PDB viewer/ Deep View allows both local homology modelling and offers integration with the Swiss Model Protein Homology Modelling Server at expasy.org
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 (Wüthrich Lab)
VMD (Visual molecular dynamics) 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. See also NAMD molecular dynamics simulator and MDtools Molecular dynamics analysis tools from the same site.

Computational und Modellvalidierungsserver

SWISS-MODEL (automatische Homologie-Modellierung von Proteinstrukturen)
SCWRL program for prediction of protein side-chain conformations, gets you from C-alpha-only structures to full protein models
Morph Server with Associated Tools for Flexibility and Geometric Analysis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis
Multi-chain Morph Server (beta-Test)
MolProbity Protein Structure Evaluation and Validation
WhatIf Protein Structure and Model Validation
PDB ADIT! Validation server
Indie - Morph a molecule
MolInspiration Calculation of Molecular Properties
EMBO Bioinformatics Course on Model Validation
The ConSurf server (Identification of Functional Regions in Proteins through sequence conservation )
ProDrg2 Zeichnung eines kleinen Moleküls-> GROMOS energy minimized coordinate file

User's Group

For many of the Molecular Visualization and Molecular Modelling Programms presented on this CD, active User's groups discuss features and bugs of the programs and can be very helpful if you run into problems. If you can not solve a problem with the information presented on the program's webpage and user's manual, search the user's group archive and if you still can't find the answer, post your question to the user's group. Subscribing to the User's group can give you a lot of information on who does what with the program.