ConSurf 2016 – Identification of Functional Regions in Proteins

ConSurf 2016

:: DESCRIPTION

The ConSurf server is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I., Pupko T., and Ben-Tal N. 2016
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Nucl. Acids Res. 2016; DOI: 10.1093/nar/gkw408; PMID: 27166375

Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucl. Acids Res. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830

SOLart 1.0 – Protein Solubility Prediction

SOLart 1.0

:: DESCRIPTION

SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics, 36 (5), 1445-1452 2020 Mar 1
SOLart: A Structure-Based Method to Predict Protein Solubility and Aggregation
Qingzhen Hou , Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci

SCooP 1.0 – Prediction of the Stability Curve of Proteins

SCooP 1.0

:: DESCRIPTION

SCooP is a fast and accurate method for predicting the Gibbs-Helmholtz equation associated to the folding transition of a target protein of known (or modeled) structure. In addition, SCooP yields an estimation of the thermodynamic quantities that characterize the folding process, in particular the change in enthalpy and in heat capacity upon folding, the melting temperature and the folding free energy at room temperature.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Pucci, J.M. Kwasigroch, M. Rooman (2017),
SCooP : an accurate and fast predictor of protein stability curves as a function of the temperature,
Bioinformatics 33, 3415-3422.

BRAGI 20091106 – A Protein Visualization and Modeling Program

BRAGI 20091106

:: DESCRIPTION

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs.

::DEVELOPER

BRAGI Team

:: SCREENSHOTS

BRAGI

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 BRAGI

:: MORE INFORMATION

Citation

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW.
Bioinformatics. 2005 Apr 1;21(7):1291-3. Epub 2004 Nov 16.

CRNPRED 1.1 – Predict Secondary Structures of Protein

CRNPRED 1.1

:: DESCRIPTION

CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence.

CRNPRED Online Version

::DEVELOPER

CRNPRED team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CRNPRED

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Sep 5;7:401.
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.
Kinjo AR, Nishikawa K.

PDBjViewer 4.5.5 – Display 3D Molecular Graphics of Proteins and Nucleic Acids

PDBjViewer 4.5.5

:: DESCRIPTION

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.

::DEVELOPER

PDBjViewer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java
  • JOGL

:: DOWNLOAD

 PDBjViewer

:: MORE INFORMATION

Citation

Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.
eF-site and PDBjViewer: database and viewer for protein functional sites.
Kinoshita K, Nakamura H.

OSCAR – Protein Side Chain Modeling

OSCAR

:: DESCRIPTION

OSCAR (Optimized Side Chain Atomic eneRgy) is a software of new force fields for protein side chain modeling

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 OSCAR

:: MORE INFORMATION

Citation

J Comput Chem. 2011 Jun;32(8):1680-6. doi: 10.1002/jcc.21747.
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.
Liang S, Zhou Y, Grishin N, Standley DM.

Multi-VORFFIP / VORFFIP – Predicts protein-, peptide-, DNA- and RNA-binding sites in Proteins

Multi-VORFFIP / VORFFIP

:: DESCRIPTION

Multi-VORFFIP is a structure-based, machine learning, computational method designed to predict protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. M-VORFFIP integrates a wide and heterogeneous set of residue- and environment-based information using a two-step Random Forest ensemble classifier.

VORFFIP (Voronoi Random Forest Feedback Interface Predictor) is structure-based computational method for prediction of protein binding sites.

::DEVELOPER

 Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 15;28(14):1845-50. doi: 10.1093/bioinformatics/bts269. Epub 2012 May 4.
A holistic in silico approach to predict functional sites in protein structures.
Segura J1, Jones PF, Fernandez-Fuentes N.

BMC Bioinformatics. 2011 Aug 23;12:352. doi: 10.1186/1471-2105-12-352.
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams.
Segura J1, Jones PF, Fernandez-Fuentes N.

Phos3D – Prediction of Phosphorylation Sites (P-sites) in Proteins

Phos3D

:: DESCRIPTION

Phos3D is a web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial context of experimentally identified P-sites.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Apr 21;10:117.
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
Durek P, Schudoma C, Weckwerth W, Selbig J, Walther D.

Jali 1.3 – Remote Homology Detection for Protein

Jali 1.3

:: DESCRIPTION

Jali (Jumping Alignments) is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.

::DEVELOPER

Jens Stoye

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Jali

:: MORE INFORMATION

Citation

A novel approach to remote homology detection: Jumping Alignments
R. Spang, M. Rehmsmeier, J. Stoye
J. Comp. Biol., volume 9, pp. 747-760, 2002