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Alpha helix - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Alpha_helix

Beta sheet - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Beta_sheet

N-terminus (Beta sheet) - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/N-terminal_end

C-terminus (Beta sheet) - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/C-terminal_end

AAindex: Amino acid index database
http://www.genome.jp/aaindex/

Amino Acid Properties
http://www.geneinfinity.org/sp/sp_aaprops.html

Amino Acids
http://www.elmhurst.edu/%7Echm/vchembook/561aminostructure.html

Amino acid substitution, sequence alignment, amino acids, replacement matrix, replacement matrices
http://www.proteinstructures.com/Sequence/Sequence/amino-acid-substitution.html

Amino Acid Browser - ala
http://bmrb.wisc.edu/referenc/commonaa.php

Hydropathicity Plots
http://arbl.cvmbs.colostate.edu/molkit/hydropathy/index.html

Protein Calculator
http://www.scripps.edu/%7Ecdputnam/protcalc.html

pKa and LogP Measurements
http://www.raell.demon.co.uk/chem/logp/logppka.htm

Protein kinase A - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Protein_kinase_A

Proteinogenic amino acid - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/List_of_standard_amino_acids

Residue Tables
http://bmrb.wisc.edu/referenc/aa_tables.html

Structural motif - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Structural_motif

Smith–Waterman algorithm - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

Van der Waals force - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Van_der_Waals_force

Text based summary of protein properties (great for scriptwriters!)
http://bmrb.wisc.edu/ref_info/aadata.dat

Online Book: Chapter 2: Protein Structure and Function
http://www.web-books.com/MoBio/Free/Chap2.htm

Tutorial: Homology modelling for beginners, Amino Acid Properties
http://swift.cmbi.kun.nl/swift/future/aainfo/

Publication:
TBioMed | Full text | Amino acid size, charge, hydropathy indices and matrices for protein structure analysis
http://www.tbiomed.com/content/3/1/15

Software Solution:
BLAST - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/BLAST

Download BLAST Software and Databases Documentation
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

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