Membrane protein prediction methods.

TitleMembrane protein prediction methods.
Publication TypeJournal Article
Year of Publication2007
AuthorsPunta, M, Forrest, LR, Bigelow, H, Kernytsky, A, Liu, J, Rost, B
Date Published2007 Apr
KeywordsBiochemistry, Databases, Factual, Genomics, Membrane Proteins, Models, Chemical, Predictive Value of Tests, Protein Conformation, Structure-Activity Relationship

We survey computational approaches that tackle membrane protein structure and function prediction. While describing the main ideas that have led to the development of the most relevant and novel methods, we also discuss pitfalls, provide practical hints and highlight the challenges that remain. The methods covered include: sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling. In general, predictions of functional and structural features of membrane proteins are improving, although progress is hampered by the limited amount of high-resolution experimental information available. While predictions of transmembrane segments and protein topology rank among the most accurate methods in computational biology, more attention and effort will be required in the future to ameliorate database search, homology and ab initio modeling.

Alternate JournalMethods
PubMed ID17367718
PubMed Central IDPMC1934899
Grant ListR01 LM007329-01A1 / LM / NLM NIH HHS / United States
R01-GM64633-01 / GM / NIGMS NIH HHS / United States
R01-LM07329-01 / LM / NLM NIH HHS / United States
U54-GM75026-01 / GM / NIGMS NIH HHS / United States