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Structural > Model Building

DNA is a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame.
ARP/wARP is a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.
Coot (Crystallographic Object-Oriented Toolkit) is for model building, model completion, and validation.
DINO is a realtime 3D visualization program for structural biology data.
Insight II
Insight II provides a comprehensive, integrated molecular graphics environment for visualization, protein engineering, macromolecular simulations, homology modeling, and de novo ligand design, enabling researchers to gain early insights into the structure and function of their targets of interest.
MAIN is a very powerful program and a programming language which provides tools in the form of macros to diagnose many of your crystallographical problems.
MIFit was originally developed by Duncan McRee as a replacement for his popular xfit program.
The menu-driven operation of NOC makes it easy to use and flexible environment to explore macromolecular structures.
O is a macromolecular crystallographic modeling tool by Alwyn Jones.
SOLVE: Automated crystallographic structure solution for MIR, SAD, and MAD; RESOLVE: Statistical density modification, local pattern matching, automated model-building, automated ligand-fitting, and prime-and-switch minimum bias phasing
SYBYL is a suite of computational informatics software designed to enhance the drug discovery workflows and decision-making of today's computational chemists and molecular modelers.
Symmetry Equivalent Molecules
A web based GUI to generate and visualize the macromolecules.
Turbo-Frodo is a general-purpose molecular modeling environment.
Uppsala Software Factory (Gerard Kleywegt)
Gerard Kleywegt's site (USF) with programs and other links handy for macromolecular crystallography.
WHAT IF is a versatile molecular modeling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
XtalView is a complete package for solving a macromolecular crystal structures (not currently supported).