NUCLEOSOME TOUR: Interactive presentation of a Standard Nucleosome (1eqz.pdb) by Yinhuai Chen.

Exploration and comparison of the S. cerevisiae nucleosome with a modeled Cse4p (centromeric) octamer by Kelcy J. Newell: Interactive Chime presentation in protein explorer (PIPE) in which the S. cerevisiae nucleosome crystal structure (1id3.pdb) is utilized as a template to produce a homology modeled centromeric octamer which replaces histone H3 with Cse4p.

*In order to see this presentation you must be using a Netscape browser and have the CHIME plugin.

Histone Sequence Database: The Histone Database is a searchable, periodically updated collection of histone fold-containing sequences derived from sequence-similarity searches of public databases. Sequence sets are presented in redundant and non-redundant FASTA form, hotlinked to GenBank sequence files.

Archaeal Histone Database: An interesting database about these primitive histones found in archae-bacteria.

Protein Databank: The worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

Protein Explorer: Free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. Authored by Dr. Eric Martz here at Umass Amherst, it is arguably the easiest-to-use software of its kind. There are specific browser requirements for using PE.

Deep View Swiss-PdbViewer: Freeware that allows analysis of changes to PDB files. This software is incredibly powerful and is also used in conjunction with Swiss Model to help in the amino acid alignment and production of oligomeric homology models.

Saccharomyces Genome Database: Check out the annotatated S. cerevisiae genome database. An important tool for a yeast lab.

The "Génolevures" project: a large-scale comparative genomics project between Saccharomyces cerevisiae and 14 other yeast species representative of the various branches of the Hemiascomycetous class.

National Center for Biotechnology Information (NCBI): national resource for molecular biology information.

ExPASy Molecular Biology Server: 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.

NCBI - Protein: national resource for molecular biology information.

Protein Explorer: Free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. Authored by Dr. Eric Martz here at Umass Amherst, it is arguably the easiest-to-use software of its kind. There are specific browser requirements for using PE.

Swiss Model: a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

Deep View Swiss-PdbViewer: Freeware that allows analysis of changes to PDB files. This software is incredibly powerful and is also used in conjunction with Swiss Model to help in the amino acid alignment and production of oligomeric homology models.

The WHAT IF Web Interface: Another server for homology models with many other resources for evaluating both you model AND your template structure.

3D Jury Meta Server: provides access to various fold recognition and local structure prediction methods.

Judging the Quality of Macromolecular Models: A Glossary of Terms from Crystallography, NMR, and Homology Modeling

The WHAT IF Web Interface: resources for evaluating both you model AND your template structure.

Biotech Validation Suite for Protein Structures: Performs PROCHECK V3.5, PROVE V2.3 and WHAT IF V4.99 checks upon the submitted structure.

Verify3D Structure Evaluation Server

ProQ - Protein quality prediction

Validation Of Structural Models: The Richardson Lab kinemage site.