Fast prediction of protein domain boundaries using conserved local patterns.

Journal of Molecular Modeling
Rajani R Joshi, Vivekanand V Samant

Abstract

We have found certain conserved motifs and secondary structural patterns present in the vicinity of interior domain boundary points (dbps) by a data-driven approach without any a priori constraint on the type and number of such features, and without any requirement of sequence homology. We have used these motifs and patterns to rerank the solutions obtained by the well-known domain guess by size (DGS) algorithm. We predict, overall, five solutions. The average accuracy of overall (i.e., top five) predictions by our method [domain boundary prediction using conserved patterns (DPCP)] has improved the average accuracy of the top five solutions of DGS from 71.74 to 82.88 %, in the case of two-continuous-domain proteins, and from 21.38 to 80.56 %, for two-discontinuous-domain proteins. Considering only the top solution, the gains in accuracy are from 0 to 72.74 % for two-continuous-domain proteins with chain lengths up to 300 residues, and from 0 to 62.85 % for those with up to 400 residues. In the case of discontinuous domains, top_min solutions (the minimum number of solutions required for predicting all dbps of a protein) of DPCP improve the average accuracy of DGS prediction from 12.5 to 76.3 % in proteins with chain lengths up ...Continue Reading

References

Feb 1, 1996·Protein Science : a Publication of the Protein Society·E G Hutchinson, J M Thornton
Nov 21, 1996·Journal of Theoretical Biology·L E Stanfel
Apr 1, 1998·Protein Science : a Publication of the Protein Society·S JonesJ M Thornton
Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·C A OrengoJ M Thornton
Jun 27, 2000·Bioinformatics·L J McGuffinD T Jones
Oct 20, 2000·Bioinformatics·S J WheelanS H Bryant
Aug 22, 2001·Biopolymers·M R Betancourt, J Skolnick
Oct 9, 2002·Current Protein & Peptide Science·D XuE C Uberbacher
Nov 21, 2002·Protein Science : a Publication of the Protein Society·Russell L MarsdenDavid T Jones
Mar 26, 2003·Bioinformatics·Mikita Suyama, Osamu Ohara
Aug 21, 2003·Computational Biology and Chemistry·Rajani R Joshi, S Jyothi
Nov 5, 2003·Journal of Molecular Biology·Ashish V TendulkarChetan Y Mone
Dec 3, 2003·Journal of Structural and Functional Genomics·Takanori TanakaShigeyuki Yokoyama
Apr 15, 2004·Journal of Molecular Biology·Ashish V TendulkarPramod P Wangikar
Mar 25, 2005·Proteins·Jaehyun SimJooyoung Lee
Aug 12, 2005·Journal of Molecular Modeling·Subramanian JyothiRajani R Joshi

❮ Previous
Next ❯

Citations

Dec 7, 2007·Nucleic Acids Research·Chi N I PangRichard A George
Jan 28, 2014·Journal of Molecular Modeling·Rajani R Joshi, S Sreenath
Oct 10, 2006·Journal of Molecular Modeling·Rajani R Joshi, Vivekanand V Samant

❮ 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.