Proteins

Proteins are a particular group of linear chain polymers, built up from a collection of 20 different monomers known as amino acids. Proteins, unlike many synthetic polymers, have a very specific sequence (and hence length), which results in a specific three-dimensional structure. Presently much computational effort is dedicated to the prediction of such structure from a given sequence.

Potentials and models

• CABS model
• Chen and Imamura model
• DFIRE model
• Go potential
• Irbäck hydrogen bond model
• Nanias model
• Patchy particles
• TE-13 model

Systems

• Amelogenin
• Chymotrypsin Inhibitor 2 (CI2)
• Ubiquitin
• Villin headpiece
• Bovine pancreatic trypsin inhibitor (BPTI)

Other

• Folding@Home
• I-TASSER

General Reading

• Christian B. Anfinsen "Principles that Govern the Folding of Protein Chains", Science 181 pp. 223-230 (1973)
• Thomas E. Creighton "Proteins: Structures and Molecular Properties", W. H. Freeman, Second Edition edition (1993) ISBN 071677030X
• A.V. Yakubovich, I.A. Solov'yov, A.V. Solov'yov and W. Greiner "Phase transition in polypeptides: a step towards the understanding of protein folding", The European Physical Journal D 40 pp. 363-367 (2006)
• Arieh Ben-Naim "Some aspects of the protein folding problem examined in one-dimensional systems", Journal of Chemical Physics 135 085104 (2011)
• Arieh Ben-Naim "The Protein Folding Problem and Its Solutions", World Scientific Publishing (2013) ISBN 978-981-4436-35-9
• Arieh Ben-Naim "Myths and Verities in Protein Folding Theories", World Scientific Publishing (2016) ISBN 978-981-4725-98-9