SWISS-MODEL – Protein Structure Homology-modelling Server

SWISS-MODEL

:: DESCRIPTION

SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

::DEVELOPER

Protein Structure Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W252-8. doi: 10.1093/nar/gku340. Epub 2014 Apr 29.

QMEAN – Server for Model Quality Estimation

QMEAN

:: DESCRIPTION

The QMEAN server provides access to two scoring functions for the quality estimation of protein structure models which allow to rank a set of models and to identify potentially unreliable region within these.

::DEVELOPER

Protein Structure Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Feb 1;27(3):343-50. doi: 10.1093/bioinformatics/btq662. Epub 2010 Dec 5.
Toward the estimation of the absolute quality of individual protein structure models.
Benkert P1, Biasini M, Schwede T.

lDDT – Comparing Protein Structures and Models using Distance Difference Tests

lDDT

:: DESCRIPTION

The lDDT (local Distance Difference Test) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.

::DEVELOPER 

lDDT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2722-8. doi: 10.1093/bioinformatics/btt473. Epub 2013 Aug 27.
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
Mariani V1, Biasini M, Barbato A, Schwede T.

FunFOLD 3.0 – Protein-Ligand Binding Site Prediction Server

FunFOLD 3.0

:: DESCRIPTION

The FunFOLD software is freely available as both a standalone package and a prediction server, providing competitive ligand binding site residue predictions for expert and non-expert users alike. The software provides a new fully automated approach for structure based function prediction using 3D models of proteins.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 FunFOLD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 16;12:160. doi: 10.1186/1471-2105-12-160.
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.
Roche DB1, Tetchner SJ, McGuffin LJ.

ModFOLD 6 – Model Quality Assessment Server

ModFOLD 6

:: DESCRIPTION

The ModFOLD server is the latest version of server for the estimation of both the global and local (per-residue) quality of 3D protein models.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModFOLD

:: MORE INFORMATION

Citation

Maghrabi, A.H.A. & McGuffin, L.J. (2017)
ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins,
Nucleic Acids Res. 2017 Jul 3;45(W1):W416-W421. doi: 10.1093/nar/gkx332.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W368-72. doi: 10.1093/nar/gkt294. Epub 2013 Apr 25.
The ModFOLD4 server for the quality assessment of 3D protein models.
McGuffin LJ1, Buenavista MT, Roche DB.

PeptideBuilder 1.0.4 – Python Library to Generate Model Peptides

PeptideBuilder 1.0.4

:: DESCRIPTION

PeptideBuilder is a simple Python library to construct models of polypeptides from scratch.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 PeptideBuilder

:: MORE INFORMATION

Citation

Tien MZ, Sydykova DK, Meyer AG, Wilke CO. (2013)
PeptideBuilder: A simple Python library to generate model peptides.
PeerJ 1:e80

FEATURE 3.1 – Examine Biological Structures

FEATURE 3.1

:: DESCRIPTION

FEATURE is an automated tools that examines biological structures and produces useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical/pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering).

::DEVELOPER

FEATURE Team

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 FEATURE

:: MORE INFORMATION

Citation:

Halperin I, Glazer DS, Wu S, Altman RB.
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications.”
BMC Genomics. 9 Suppl 2 S2.

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.

Spanner – Hybrid-template Structural Modeling

Spanner

:: DESCRIPTION

Spanner is a structural homology modeling program that threads a query amino-acid sequence onto a template protein structure. Spanner is unique in that it handles gaps by spanning the region of interest using fragments of known structures.

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

No

:: MORE INFORMATION

Citation

Immunome Res. 2011 Apr 1;7(1):1-8.
Bridging the gap between single-template and fragment based protein structure modeling using Spanner.
Lis M, Kim T, Sarmiento JJ, Kuroda D, Dinh HV, Kinjo AR, Amada K, Devadas S, Nakamura H, Standley DM.

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.