JPred: a consensus secondary structure prediction server

Sequence–structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

Download Full-text

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)

Bioinformatics ◽

10.1093/bioinformatics/btm379 ◽

2007 ◽

Vol 23 (19) ◽

pp. 2628-2630 ◽

Cited By ~ 22

Author(s):

H. Cheng ◽

T. Z. Sen ◽

R. L. Jernigan ◽

A. Kloczkowski

Keyword(s):

Data Mining ◽

Secondary Structure ◽

Structure Prediction ◽

Secondary Structure Prediction ◽

Protein Secondary Structure ◽

Database Mining ◽

Protein Secondary Structure Prediction ◽

Prediction Server

Download Full-text

JPred4: a protein secondary structure prediction server

Nucleic Acids Research ◽

10.1093/nar/gkv332 ◽

2015 ◽

Vol 43 (W1) ◽

pp. W389-W394 ◽

Cited By ~ 860

Author(s):

Alexey Drozdetskiy ◽

Christian Cole ◽

James Procter ◽

Geoffrey J. Barton

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Secondary Structure Prediction ◽

Protein Secondary Structure ◽

Protein Secondary Structure Prediction ◽

Prediction Server

Download Full-text

Computational studies on LiP H isolated from Ganoderma lucidum GD88

Archives of Biological Sciences ◽

10.2298/abs141014041p ◽

2015 ◽

Vol 67 (3) ◽

pp. 817-828

Author(s):

Nayana Parambayil ◽

Aiswarya Chenthamarakshan ◽

Arinnia Anto ◽

Sudha Hariharan ◽

Padma Nambisan

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Ganoderma Lucidum ◽

Secondary Structure Prediction ◽

Cell Wall Component ◽

Reading Frame ◽

Prediction Server ◽

Structure Stabilization ◽

H Protein

Ganoderma lucidum is a basidiomycete fungus that produces ligninase for the modification of lignin. Lignin peroxidase (LiP) is a glycoprotein that acts on the recalcitrant cell wall component lignin. In the present study, the phylogenetic analysis of Ganoderma lucidum GD88 with the partial coding sequence (cds) of other LiP isoforms was performed using MEGA6. After determination of the open reading frame, the +3 frame nucleotide sequence was converted to protein using the EMBOSS Transseq and the secondary structure was predicted using the Chou and Fasman Secondary Structure Prediction server (CFSSP). Protein modeling was also performed by SWISS-MODEL. The obtained result shows that the lipH partial cds of Ganoderma lucidum GD88 is homologous to the lipD gene of Phanerochaete chrysosporium. The secondary structure prediction result revealed that the percent content of the helix (67) is higher than the percent contents of sheet (53.4) and turns (13.6). According to the generated model, LiP H protein is a homodimer with chains A and B. The heme acts as a ligand and plays a major role in structure stabilization.

Download Full-text