PredictProtein 2013 – Protein Sequence Analysis, Prediction of Structural and Functional Features

PredictProtein 2013

:: DESCRIPTION

PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges. Listed below is a comprehensive list of methods and databases currently incorporated into the server.

::DEVELOPER

Rost Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PredictProtein

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 May 5
PredictProtein–an open resource for online prediction of protein structural and functional features.
Yachdav G1, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T,  nigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost AB.

SAGPAR – StructurAl Grammar-based automated PAthway Reconstruction

SAGPAR

:: DESCRIPTION

SAGPAR is a fast and robust algorithm that generates any metabolic pathway using some given structural representations of metabolites.

::DEVELOPER

Dr. Rajat Kumar De

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SAGPAR

:: MORE INFORMATION

Citation:

Interdiscip Sci. 2012 Jun;4(2):116-27. doi: 10.1007/s12539-012-0119-8. Epub 2012 Jul 29.
SAGPAR: structural grammar-based automated pathway reconstruction.
Tagore S1, De RK.

CopySeq 1.7.1 – Discovery and Copy-number Genotyping of Genomic Structural Variants

CopySeq 1.7.1

:: DESCRIPTION

CopySeq is a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

::DEVELOPER

Korbel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Jim Kent’s twoBitToFa program (available here)
  • SAMtools

:: DOWNLOAD

 CopySeq

:: MORE INFORMATION

Citation

Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, et al. (2010)
Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity.
PLoS Comput Biol 6(11): e1000988.

SEMPHY 2.0 b3 – Structural EM Phylogenetic Reconstruction

SEMPHY 2.0 b3

:: DESCRIPTION

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.

::DEVELOPER

Nir Friedman’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX

:: DOWNLOAD

  SEMPHY

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jan 15;23(2):e136-41.
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
Ninio M, Privman E, Pupko T, Friedman N.

Fr-TM-align 201307 – Protein Structural Alignment

Fr-TM-align 201307

:: DESCRIPTION

Fr-TM-align is a program for protein structural alignment. It is one of the latest developments based on TM-align.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Fr-TM-align

:: MORE INFORMATION

Citation

Pandit, S B, Skolnick J. 2008.
Fr-TM-align: A new protein structural alignment method based on fragment alignments and the TM-score.
BMC bioinformatics. 9:531.

CDK 1.4.19 – Java Library for Structural Chemo- & Bioinformatics

CDK 1.4.19

:: DESCRIPTION

CDK (The Chemistry Development Kit) is a Java library for structural chemo- and bioinformatics.The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.

::DEVELOPER

CDK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

CDK

:: MORE INFORMATION

Citation:

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics“.
Steinbeck C., Han Y., Kuhn S., Horlacher O., Luttmann E., Willighagen E.L.,
J. Chem. Inf. Comput. Sci. 2003 Mar-Apr; 43(2):493-500 (DOI: 10.1021/ci025584y)

Recent Developments of the Chemistry Development Kit (CDK) – An Open-Source Java Library for Chemo- and Bioinformatics“.
Steinbeck C., Hoppe C., Kuhn S., Floris M., Guha R., Willighagen E.L.,
Curr. Pharm. Des. 2006; 12(17):2111-2120 (DOI: 10.2174/138161206777585274)