Protein structure prediction

Biochimie
J Garnier

Abstract

Current methods developed for predicting protein structure are reviewed. The most widely used algorithms of Chou and Fasman and Garnier et al for predicting secondary structure are compared to the most recent ones including sequence similarity methods, neural network, pattern recognition or joint prediction methods. The best of these methods correctly predict 63-65% of the residues in the database with cross-validation for 3 conformations, helix, beta strand and coli with a standard deviation of 6-8% per protein. However, when a homologous protein is already in the database, the accuracy of prediction by the similarity peptide method of Levin and Garnier reaches about 90%. Some conclusions can be drawn on the mechanism of protein folding. As all the prediction methods only use the local sequence for prediction (+/- 8 residues maximum) one can infer that 65% of the conformation of a residue is dictated on average by the local sequence, the rest is brought by the folding. The best predicted proteins or peptide segments are those for which the folding has less effect on the conformation. Presently, prediction of tertiary structure is only of practical use when the structure of a homologous protein is already known. Amino acid alig...Continue Reading

References

Nov 5, 1978·Journal of Molecular Biology·J Janin, S Wodak
Jan 1, 1990·Proteins·I T Weber
Nov 1, 1989·Journal of Molecular Recognition : JMR·J CherfilsD Kahn
Dec 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·A C MartinA R Rees
Jul 1, 1989·Trends in Biochemical Sciences·G D Fasman
Dec 21, 1989·Nature·C ChothiaW R Tulip
Apr 1, 1989·Computer Applications in the Biosciences : CABIOS·R RechidP Argos
Jan 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·L H Holley, M Karplus
Aug 20, 1988·Journal of Molecular Biology·N Qian, T J Sejnowski
Sep 1, 1988·Protein Engineering·V BiouJ Garnier
Aug 1, 1988·Computer Applications in the Biosciences : CABIOS·O Gascuel, J L Golmard
Jun 20, 1987·Journal of Molecular Biology·M J ZvelebilM J Sternberg
Jan 14, 1986·Biochemistry·F E CohenR J Fletterick
Nov 5, 1983·Journal of Molecular Biology·M Levitt
Jun 10, 1983·Science·C S CraikR Fletterick
Jan 1, 1983·Annual Review of Biophysics and Bioengineering·N Go
May 8, 1983·FEBS Letters·W Kabsch, C Sander
Jan 1, 1982·Annual Review of Biophysics and Bioengineering·M Levitt
May 13, 1983·Science·S KirkpatrickM P Vecchi

❮ Previous
Next ❯

Citations

Jan 7, 1998·Protein Science : a Publication of the Protein Society·S Parthasarathy, M R Murthy
Jan 1, 1992·Pharmacology & Therapeutics·J M Chalovich
Mar 7, 1996·Biophysical Chemistry·G Böhm
Dec 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·A S GreenbergA R Kimmel
Jan 4, 1994·Proceedings of the National Academy of Sciences of the United States of America·L JinJ A Wells
Jul 19, 1994·Proceedings of the National Academy of Sciences of the United States of America·Z HuangF E Cohen
Jan 1, 1993·SAR and QSAR in Environmental Research·M Reczko
Jun 7, 2005·Physical Chemistry Chemical Physics : PCCP·Pooja NarangB Jayaram
May 1, 2017·Wiley Interdisciplinary Reviews. Computational Molecular Science·Michael Feig
Apr 1, 1995·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·R C Yu, T Head-Gordon
Jun 28, 1996·The Journal of Biological Chemistry·W MiaoM S Marshall
Jun 1, 1992·Journal of Bacteriology·M LonettoC A Gross
Jun 1, 1992·Cell Calcium·R H Kretsinger
Jun 5, 1992·Journal of Molecular Biology·S M Muskal, S H Kim
May 29, 2014·Journal of Chemical Information and Modeling·Jan Zacharias, Ernst-Walter Knapp

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.