14-3-3-Pred – Webserver to predict 14-3-3-binding sites in Proteins

14-3-3-Pred

:: DESCRIPTION

14-3-3-Pred is a webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides.
Madeira F, Tinti M, Murugesan G, Berrett E, Stafford M, Toth R, Cole C, MacKintosh C, Barton GJ.
Bioinformatics. 2015 Mar 3. pii: btv133.

DynDom 1.5 / DynDom3D 1.04 – Protein Domain Motion Analysis

DynDom 1.5 / DynDom3D 1.04

:: DESCRIPTION

DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

DynDom3D is a new program for the analysis of domain movements in large, multi-chain, biomolecular complexes.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • fortran compiler

:: DOWNLOAD

 DynDom , DynDom3D

:: MORE INFORMATION

Citation

Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50.
Hayward S, Lee RA.
J Mol Graph Model. 2002 Dec;21(3):181-3.

Bioinformatics. 2003 Jul 1;19(10):1290-1.
The DynDom database of protein domain motions.
Lee RA, Razaz M, Hayward S.

SMART 8.0 – Analysis of Protein Domain Architectures

SMART 8.0

:: DESCRIPTION

SMART (Simple Modular Architecture Research Tool) is an online resource for the identification and annotation of protein domains and the analysis of protein domain architectures.More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Letunic I, Doerks T, Bork P
SMART: recent updates, new developments and status in 2015
Nucleic Acids Res 2014; doi:10.1093/nar/gku949

Letunic et al. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res , doi:10.1093/nar/gkr931

STITCH 5.0 – Search Tool for Interactions of Chemicals and proteins

STITCH 5.0

:: DESCRIPTION

STITCH (search tool for interactions of chemicals)  is a resource to explore known and predicted interactions of chemicals and proteins.Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

 STITCH

:: MORE INFORMATION

Citation

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.
Nucleic Acids Res. 2015 Nov 20. pii: gkv1277.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M1, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P
Nucleic Acids Res. 2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.

protTrace 1.0 – Estimate Evolutionary Traceability of Protein

protTrace 1.0

:: DESCRIPTION

ProtTrace is a simulation based approach to assess for a protein, the seed, over what evolutionary distances its orthologs can be found by means of sharing a significant sequence similarity

::DEVELOPER

protTrace team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ProtTrace

:: MORE INFORMATION

Citation

The Evolutionary Traceability of a Protein.
Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I.
Genome Biol Evol. 2019 Feb 1;11(2):531-545. doi: 10.1093/gbe/evz008.

subGolgi v2.0 – Prediction of subGolgi locations of Proteins

subGolgi v2.0

:: DESCRIPTION

subGolgi is a sequence-based predictor for identifying Golgi-resident proteins and their types

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Protein Pept Lett. 2011 Jan;18(1):58-63.
Identify Golgi protein types with modified Mahalanobis discriminant algorithm and pseudo amino acid composition.
Ding H1, Liu L, Guo FB, Huang J, Lin H.

PVPred – Identification of Phage Virion Proteins

PVPred

:: DESCRIPTION

PVPred is a sequence-based tool for identifying phage virion proteins

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Biosyst. 2014 Jun 16. [Epub ahead of print]
Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis.
Ding H1, Feng PM, Chen W, Lin H.

CancerPPD – Database of Anticancer Peptides and Proteins

CancerPPD

:: DESCRIPTION

CancerPPD is a unique resource of its kind, which provides detailed information related to experimentally verified anticancer peptides (ACPs) and proteins.

::DEVELOPER

CancerPPD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CancerPPD: a database of anticancer peptides and proteins.
Tyagi A, Tuknait A, Anand P, Gupta S, Sharma M, Mathur D, Joshi A, Singh S, Gautam A, Raghava GP.
Nucleic Acids Res. 2015 Jan;43(Database issue):D837-43. doi: 10.1093/nar/gku892.

RNApin – Prediction of Protein Interacting Nucleotides in a RNA Sequence

RNApin

:: DESCRIPTION

RNApin is a Support Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.

::DEVELOPER

RNApin team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.
Panwar B, Raghava GP.
Genomics. 2015 Apr;105(4):197-203. doi: 10.1016/j.ygeno.2015.01.005

THPdb – Database of FDA approved Therapeutic Peptides and Proteins

THPdb

:: DESCRIPTION

THPdb is a manually curated repository of Food and Drug Administration (FDA) approved therapeutic peptides and proteins

::DEVELOPER

THPdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser / Android

:: DOWNLOAD

THPdb

:: MORE INFORMATION

Citation

THPdb: Database of FDA-approved peptide and protein therapeutics.
Usmani SS, Bedi G, Samuel JS, Singh S, Kalra S, Kumar P, Ahuja AA, Sharma M, Gautam A, Raghava GPS.
PLoS One. 2017 Jul 31;12(7):e0181748. doi: 10.1371/journal.pone.0181748.