WEB RESOURCES AND SOFTWARE DOWNLOAD SITES:
Software Download Sites:
Netscape Navigator (latest version HERE)(archive
site for various versions HERE)
DO NOT USE CHIME WITH INTERNET EXPOLORER.
Rasmol 2.7.1 download and manual HERE
General Rasmol/Chime homepage HERE
Hypertext reference manual for version 2.6.2 (HERE)
Chime download (get Chime 2.0 or greater) HERE
Kinemage (Mage and Prekin) software can be downloaded HERE
A few starting points as sources for information:
RCSB database of PDB files
ENTREZ search engine: allows searches of PubMed (Medline reference database), Nucleotide (DNA/RNA sequences from GenBank), Protein (protein sequences from GenBank), Genome (complete genome sequence information), Structure (a different structural database than RCSB), PopSet (a database of population sequences.
In addition be sure to check OMIM for human disease information.
BLAST, PSI-BLAST and PHI-BLAST searches for identifying related sequences.
Remember: many of these databases are linked to each other so additional reference and resource information is just a mouse click away.
Additional resources:
Databases:
SCOP: Structural Classification of Proteins
CATH: Protein Structure Classification
CAZY: Carbohydrate-Active enZYmes
ENZYME: Enzyme nomenclature database
Analysis Tools:
ExPASy: Expert Protein Analysis System
BioInformatics Tools: Atelier BioInformatique Online Analysis tools
Enzyme structure databases: from Biomolecular Structure and Modelling group at University College London.
A very comprehensive resource for all sorts of analytical resource tools for sequence analysis can be found HERE.
Tools for CHIME script design:
SChiSM© - Create Webpage Annotation of Molecular Models Using Chime
Programs for Structure Modeling and Sequence Alignment/Phylogeny:
Network Protein Sequence Analysis
A Structure and Modelling Group at University College London
Database of Macromolecular Movements with Associated Tools for Geometric Analysis
World Index of Molecular Visualization Resources
Publisher Sites:
Interactive Biochemistry by Edward K. O'Neil and Charles M. Grisham at the University of Virginia
Biochemistry in 3D-Lehninger Principles of Biochemistry
College Molecular Structure Sites:
Biomolecules at Kenyon College: Molecular Biology Tutorials by BIOL 363 students and faculty
Structural Analysis at Cabrillo College
Kinase Structure Resources:
PROTEIN KINASES 3-D Structure Summary
Resource Indexes:
Biotechnology Information Directory: The WWW Virtual Library