CUBIC: Columbia University Bioinformatics Center
Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic protein structure prediction servers, and DSSPcont for continuous assignment of protein secondary structure.
http://cubic.bioc.columbia.edu/

The Vienna RNA Package
Free software for RNA secondary structure prediction, structure comparison, and sequence design.
http://www.tbi.univie.ac.at/~ivo/RNA

STRAP
Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
http://www.charite.de/bioinf/strap

PrimeColor Software
Provides freeware such as CAESAR 1.0, CAESAR 2.0, SAMOA 1.0, XT PRO, and JFinder as computational chemistry tools to study molecular structure, crystal structure, electronic structure and band structure.
http://www.primec.com

WhatIf
Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Links to the documentation in HTML. Commercial software.
http://www.cmbi.ru.nl/whatif/

Bridge Rating and Analysis of Structural Systems - BRASS
Family of computer programs for structure design and analysis of bridges. Developed by the Wyoming Department of Transportation.
http://dot.state.wy.us/web/brass/index.html

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
by R. Durbin, S.R. Eddy, A. Krogh, G.J. Mitchison. Focus is mainly on machine learning methods for alignment, phylogeny, and RNA structure analysis.
http://www.binf.ku.dk/users/krogh/books.html

Protein Structure and Function (Petsko and Ringe)
Protein Structure and Function is an introduction for postgenomic biologists to the structural basis for the biological activities of proteins, including folding and stability, the different classes of fold, and the prediction of function from structure
http://www.new-science-press.com/browse/protein/

Heise, David R.
Indiana University. This site offers an ebook on causal analysis, papers on methodology and on social psychology, and links to sites dealing with affect control theory and event structure analysis.
http://php.indiana.edu/~heise/

Journal of Social Structure
The Online Journal of Social Sciences
http://www.cmu.edu/joss/