Site Map: 3D Protein Structure & Kinemage Web Site

FTP

Site Map for
3D Protein Structure & Kinemage Web Site

Structure Validation

Kinemage

MolProbity is our new WWW server application which implements a subset of the Mage - Probe all-atom contacts functionality. We invite you to try it out so as to introduce yourself to the Reduce/Probe-Prekin/Mage software and the analysis method, without having to downlaad and install the software. Click any of the MolProbity icons that you see to go to the starting page for this application.

Model Assessment

All-Atom Contacts Analysis - add the hydrogens and then assess, view and perhaps correct atomic clashes.

Asn, Gln & His flips - use of all-atom contact analysis and H-bond networks to assess orientation of sidechains.

Ramachandran Revisit - fine detail of the Ramachandran plots as revealed by a high-quality, large database.

Crystallographic Rebuilding

Use Reduce to add & optimize hydrogens.

Use Probe and associated shell scripts to calculate and display all-atom contacts.

Probe can interface with O or XtalView.

Rotamer libraries are available for XtalView or O.

General description of Mage and Prekin and links to the download page.

Links to sources of already made kinemages.

Links to examples of the use of Mage as a teaching tool.

Examples of the use of Mage for studying/displaying other than biological macromolecules

Resources on learning how to make kinemages.

A "reasonably comprehensive" listing of kinemages on our FTP site, developed by us and others, which tutor and show the use of Mage.

JavaMage

Software Pages

The Java Mage Page

Example of and introduction to Java Mage.

Java Mage Instructions

How to use MageJava on your webpages.

Examples of MageJava kinemages:

All-atom contacts (Probe):
- for Asn/Gln flips, and
- for nucleic acid base pairing

Teaching - 3D literacy

Non-molecular javamages:
- a spinnable, clickable world globe, and
- a geodesic dome builder's kit.

Display Software

Mage - displays, and edits, kinemage graphics

JavaMage - displays kinemages on the Web

Prekin - makes molecular kinemages

All-Atom Contacts Software

Reduce - adds & optimizes hydrogens

Probe - calculates all-atom contacts

Various scripts which automate and extend Probe and Reduce

Utility Software

Contouring - 2D and 3D contours, on orthogonal grids

Dang - dihedral angles from PDB files

Cluster - groups interacting objects

PDBCNS - converts between PDB & CNS formats

Bndlist - finds covalent and hydrogen bonds

Atvol - molecular van der Waals volume

FTP Site

Rotamers & Other Databases

FTP Site
Our FTP site was cleaned and reorganized in December of 2001. These are now the major categories:

outgoing

Sidechain Rotamer Library

Introduction, description, and reference

the library in various formats

special considerations for Asn & Asp

background information

PDB and kinemage files for the rotamers

PDB Databases

100 high resolution structures of proteins with optimized H-atom placements.

The 500 proteins with optimized H-atom placements used for the Ramachandran-plot distributions.

The Lab's 2D Gallery

Laboratory Information

Gallery Entrance

ribonuclease A (ribbon)

prealbumin dimer

raster3D rendered TGF

Met s/c correction via all-atom contacts analysis

charybdotoxin (solid schematic)

porin barrel (ribbon, ramp)

myoglobin with heme (ribbon)

b-trefoil of ricin B

Ramachandran substructure (small world)

Some on and off ramps of the information superhighway:

Duke University

Biochemistry Department

Molecular Biophysics program

General lab stuff

Research philosophy and opportunities

How to get here

Pics of neat stuff laying about

internal lab info (needs password)

FTP