Tag: Coiled-coil

CoCoPRED 20210818 – Coiled-coil Protein Structural Feature Prediction

CoCoPRED 20210818

:: DESCRIPTION

CoCoPRED is a method of coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

CoCoPRED

:: MORE INFORMATION

Citation

Feng SH, Xia CQ, Shen HB.
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.
Bioinformatics. 2021 Oct 30:btab744. doi: 10.1093/bioinformatics/btab744. Epub ahead of print. PMID: 34718416.

LOGICOIL – Multi-state Coiled-coil Oligomeric State prediction

LOGICOIL

:: DESCRIPTION

LOGICOIL, the first algorithm to address the problem of predicting multiple coiled-coil oligomeric states from protein-sequence information alone.

::DEVELOPER

WOOLFSON lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

“LOGICOIL: Multi-state classification of coiled-coil oligomeric state.”
T. L. Vincent, P.J. Green and D. N. Woolfson.
Bioinformatics (2013) 29 (1): 69-76.

DrawCoil 1.0 – Produce Coiled-coil Helical Wheel Diagrams

DrawCoil 1.0

:: DESCRIPTION

DrawCoil is a web-based program for creating coiled-coil helical wheel diagrams.

::DEVELOPER

Grigoryan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  DrawCoil

:: MORE INFORMATION

Citation:

G. Grigoryan and A. E. Keating,
“Structural Specificity in Coiled-coil Interactions”,
Current Opinion in Structural Biology, 18(4): 477-483, 2008

CCCP – Coiled-coil Crick Parameterization

CCCP

:: DESCRIPTION

CCCP (Coiled-Coil Crick Parameterization) is a programs for fitting Crick parameters to coiled-coil structures and generations of ideal structures from parameters.

::DEVELOPER

Grigoryan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

  CCCP

:: MORE INFORMATION

Citation:

G. Grigoryan, W. F. DeGrado,
“Probing Designability via a Generalized Model of Helical Bundle Geometry“,
J. Mol. Biol., 405(4): 1079-1100 (2011)

Marcoil 1.2 – HMM-based Coiled-coil Prediction program

Marcoil 1.2

:: DESCRIPTION

MARCOIL is a hidden MARkov model-based program that predicts existence and location of potential coiled-coil domains in protein sequences.

::DEVELOPER

Mauro Delorenzi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

MARCOIL

:: MORE INFORMATION

Citation:

Bioinformatics. 2002 Apr;18(4):617-25.
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
Delorenzi M, Speed T.

Waggawagga – Coiled-coil and Single-Alpha-Helix prediction for Protein Sequences

Waggawagga

:: DESCRIPTION

Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains).

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Waggawagga: Comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains).
Simm D, Hatje K, Kollmar M.
Bioinformatics. 2014 Oct 22. pii: btu700.

pfilt 1.5 – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions

pfilt 1.5

:: DESCRIPTION

pfilt program is designed to mask out (i.e. replace amino acid characters with Xs) regions of low complexity, coiled-coil regions and regions with extremely biased amino acid compositions. For compositional biased regions,only the overrepresented amino acids are masked.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  pfilt

:: MORE INFORMATION

Citation:

Jones, D.T. & Swindells, M.B. (2002)
Getting the most from PSI-BLAST.
Trends Biochem Sci. 2002 Mar;27(3):161-4.

LearnCoil / LearnCoil-VMF – Computational Evidence for Coiled-coil-like Motifs in Histidine Kinase Linker Domains /Viral Membrane-Fusion Proteins

LearnCoil / LearnCoil-VMF

:: DESCRIPTION

The LearnCoil Histidase Kinase program uses an iterative learning algorithm to detect possible coiled-coil domains in histidase kinase receptors.

The LearnCoil-VMF program uses an iterative learning algorithm to detect coiled-coil-like regions in viral membrane-fusion proteins.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Singh M, Berger B, Kim PS, Berger JM, Cochran AG.
Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2738-43.

LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins.
Singh M, Berger B, Kim PS.
J Mol Biol. 1999 Jul 30;290(5):1031-41.

PS-COILS 1.0 – Coiled-coil Predictor

PS-COILS 1.0

:: DESCRIPTION

PSCOILS is a simple evolution of COILS and PCOILS  programs. It uses the same parameters that were developed for COILS and exploits both sequence and evolutionary information (in the form of sequence profiles).

::DEVELOPER

Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / WIndows
  • Python

:: DOWNLOAD

 PS-COILS 

:: MORE INFORMATION

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