Molecular Modeling & Visualization

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a la mode: A Ligand and Monomer Object Data Environment
[The Nucleic Acid Database Project] An environment for building models of ligand and monomer molecular components.

[more info][10379]

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B Molecular Modeling
[Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics.

[more info][13639]

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Center for Molecular Modeling
[NIH] CMM is a major supplier of molecular modeling resources and
expertise to the NIH research community. The site contains many annotated links to bioinformatics resources and tutorials.

[more info][12359]

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[CambridgeSoft] ChemDraw includes stereochemistry recognition and display, multi-page documents, ChemNMR with spectral display, and Name=Struct for instant structure generation. AutoNom creates IUPAC names from structures. ChemDraw for Excel brings chemistry to Excel. The Online menu links to ChemACX.Com for easy chemical sourcing and ordering. The ChemDraw Plugin adds chemical intelligence to your browser for querying databases and displaying data from web sites.

[more info][11122]

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DDL – Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.

[more info][13641]

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The Dundee PRODRG Server
[University of Dundee] This WWW PRODRG server will convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.

[more info][14073]

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History of Visualization of Biological Macromolecules
This interesting page traces the history of molecular visualization from wire models through the latest computer representations.

[more info][13979]

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[D. Richardson, Duke Univ.] A package of 2 programs, Prekins and Mage, that enables the user to create a 3-D image from a PDB-format coordinate file, which then can be modified.

[more info][11305]

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Macromolecular Visualization Lab
[University of Massachusetts] Eric Martz’s course in this topic. He’s the author of Protein Explorer, so he ought to know about this stuff.

[more info][12357]

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mmCIF: macromolecular Crystallographic Information File
[The Nucleic Acid Database Project] A subset of STAR, CIF format is suitable for archiving all types of text and numerical data: exploring its generality, upward compatibility, flexibility, and incorporating these in electronic publications.

[more info][10367]

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[Laboratories of Molecular Biophysics, Rockefeller University] ModView is a plugin to visualize and analyze multiple biomolecule structures and/or sequence alignments. It is also used as a database interface in several structure-sequence protein resources: ModBase (database of Comparative Protein Structure Models), LigBase (Structural Database of Aligned Ligand Binding Protein Sequences), and DBAli (database of sequence-structure alignments. ModView can be also used to view structures and sequences in Protein Data Bank.

[more info][13980]

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Molecular Docking Web
[Home page of Dr. Garrett M. Morris] Ligand-protein docking, with access to AutoDock program, important for drug design. Many links for ligands, protein structure, drug design, computational chemistry, bioinformatics.

[more info][13720]

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Molecular Graphics Manifesto
[University of Southern Maine] (Gale Rhodes) A web article on why and how to make molecular graphics an essential skill
for students in introductory biochemistry.

[more info][14044]

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Molecular Level
[University of Southern Maine] An outreach and consulting program that provides workshops and other training in molecular graphics.

[more info][11957]

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Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.

[more info][12311]

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Quality of Macromolecular Models
[University of Southern Maine] “A Glossary of Terms from Crystallography, NMR, and Homology Modeling.”

[more info][12360]

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The Representation of Molecular Models
[Univ. of Geneva] A site covering the basics of molecular modeling and image rendering techniques.

[more info][10121]

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World Index of Molecular Visualization Resources
This is a visitor-maintained website. Visitors may submit website URL’s with descriptions and cross-indexing terms. Categories include Biochemistry and inorganic chemistry tutorials, how to create Chime tutorials, resources for structural data files, and sources for visualization and modeling software.

[more info][12060]