FoldRec-C2C V1 – Protein Fold Recognition by combining Cluster-to-cluster model and Protein Similarity Network

FoldRec-C2C V1

:: DESCRIPTION

FoldRec-C2C is a predictor to globally incorporate the interactions among proteins into the prediction.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FoldRec-C2C

:: MORE INFORMATION

Citation

Shao J, Yan K, Liu B.
FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network.
Brief Bioinform. 2021 May 20;22(3):bbaa144. doi: 10.1093/bib/bbaa144. PMID: 32685972; PMCID: PMC7454262.

PredictFold-PSS-3D1D – Protein Fold Recognition Web Server

PredictFold-PSS-3D1D

:: DESCRIPTION

The PredictFold PSS-3D1D is a fold recognition server based on Protein Secondary Structure and 3D1D Profiles.

::DEVELOPER

Research Group of Dr.S.Parthasarathy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ganesan K & Parthasarathy S (2013)
PredictFold-PSS-3D1D: A Protein Fold Recognition Server for Predicting Folds from the Twilight Zone Sequences.
Current Bioinformatics. 8(5):552-556.

J Struct Funct Genomics. 2011 Dec;12(4):181-9. doi: 10.1007/s10969-011-9119-x. Epub 2011 Dec 3.
PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.
Ganesan K1, Parthasarathy S.

SSKDSP – Single Source K Diverse Shortest Paths Algorithm

SSKDSP

:: DESCRIPTION

SSDKSP is a scalable implementation of Single Source K Diverse Shortest Paths Algorithm.

::DEVELOPER

Lei Xie

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • JRE

:: DOWNLOAD

 SSKDSP

:: MORE INFORMATION

Citation

Protein-fold recognition using an improved single-source K diverse shortest paths algorithm.
Lhota J, Xie L.
Proteins. 2016 Apr;84(4):467-72. doi: 10.1002/prot.24993.

SAXSTER – SAXS-assisted Protein Fold Recognition

SAXSTER

:: DESCRIPTION

SAXSTER is a new algorithm to combine small-angle x-ray scattering (SAXS) data and threading for high-resolution protein structure determination. Given a query sequence, SAXSTER first generates a list of template alignments using the MUSTER threading program from the PDB library. The SAXS data will then be used to prioritize the best template alignments based on the SAXS profile match, which are finally used for full-length atomic protein structure construction

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borwser
:: DOWNLOAD

 NO 

:: MORE INFORMATION

Citation

Biophys J. 2011 Dec 7;101(11):2770-81. doi: 10.1016/j.bpj.2011.10.046.
Improving protein template recognition by using small-angle x-ray scattering profiles.
dos Reis MA1, Aparicio R, Zhang Y.

pGenTHREADER 8.9 – Protein Fold Recognition by Profile-profile Threading

pGenTHREADER 8.9

:: DESCRIPTION

pGenTHREADER and pDomTHREADER is two improved versions of the GenTHREADER protocol  for recognizing and aligning protein sequences and demonstrate their application to structure prediction and superfamily discrimination. The two versions use the same core alignment algorithm and in both cases accept features derived from common inputs: protein sequence profiles and structural information. However, the representation and combinations of these features differ between the methods and scoring and confidence values have been tuned to optimize performance in each application domain.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pGenTHREADER

:: MORE INFORMATION

Citation:

Lobley, A., Sadowski, M.I. & Jones, D.T. (2009)
pGenTHREADER and pDomTHREADER:New Methods For Improved Protein Fold Recognition and Superfamily Discrimination.
Bioinformatics. 25, 1761-1767.

TAXFOLD – Improve Toxonomy-based Protein Fold Recognition

TAXFOLD

:: DESCRIPTION

TAXFOLD is a new taxonomy-based protein fold recognition method. It extensively exploits the sequence evolution information from PSI-BLAST profiles and the secondary structure information from PSIPRED profiles. A comprehensive set of 137 features is constructed, which allows for the depiction of both global and local characteristics of PSI-BLAST and PSIPRED profiles.

::DEVELOPER

Chen Xin , Yang Jian-Yi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TAXFOLD

:: MORE INFORMATION

Citation

Jian-Yi Yang and Xin Chen,
Improving taxonomy-based protein fold recognition by using global and local features,
Proteins: Structure, Function, and Bioinformatics Volume 79, Issue 7, pages 2053–2064, July 2011

THREADER 3.51 – Protein Fold Recognition by Threading

THREADER 3.51

:: DESCRIPTION

THREADER is a software of threading which is an approach to fold recognition which used a detailed 3-D representation of protein structure. The idea was to physically “thread” a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 THREADER

:: MORE INFORMATION

Citation:

Jones, D.T., Miller, R.T. & Thornton, J.M. (1995)
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Proteins. 23, 387-397.