VisualCNA 1.0 – Constraint Network Analysis and Protein Engineering

VisualCNA 1.0

:: DESCRIPTION

VisualCNA is a PyMOL plug-in for interactive Constraint Network Analysis and protein engineering for improving thermostability

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

VisualCNA

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

 VisualCNA

:: MORE INFORMATION

Citation

VisualCNA: A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability.
Rathi PC, Mulnaes D, Gohlke H.
Bioinformatics. 2015 Mar 12. pii: btv139.

PocketAnalyzerPCA 1.30 – Pocket-space Maps to Identify novel Binding-site Conformations in Proteins

PocketAnalyzerPCA 1.30

:: DESCRIPTION

PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PocketAnalyzerPCA

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Oct 24;51(10):2666-79. doi: 10.1021/ci200168b. Epub 2011 Sep 30.
Pocket-space maps to identify novel binding-site conformations in proteins.
Craig IR1, Pfleger C, Gohlke H, Essex JW, Spiegel K.

NMSim – Modeling Macromolecular Conformational Transitions

NMSim

:: DESCRIPTION

NMSim is a normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W310-6. doi: 10.1093/nar/gks478. Epub 2012 Jun 4.
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.
Krüger DM1, Ahmed A, Gohlke H.

PowerFit 2.0.0 – Rigid body fitting of Atomic Strucures in Cryo-electron Microscopy Density Maps

PowerFit 2.0.0

:: DESCRIPTION

PowerFit is a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Python

:: DOWNLOAD

PowerFit

:: MORE INFORMATION

Citation

The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.
van Zundert GC, et al.
J Mol Biol, 429 (3), 399-407 2017 Feb 3

SpotOn – Determination of Hot-Spots at Protein-protein interfaces

SpotOn

:: DESCRIPTION

SpotOn is a robust algorithm developed to identify and classify the interfacial residues as Hot-Spots (HS) and Null-Spots (NS) with a final accuracy of 0.95 and a sensitivity of 0.95 on an independent test set.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.
Moreira IS, et al.
Sci Rep, 7 (1), 8007 2017 Aug 14

3D-DART – DNA Structure Modelling Server

3D-DART

:: DESCRIPTION

The 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool) provides a convenient means of generating custom 3D structural models of DNA with control over the local and global conformation.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

M. van Dijk and A.M.J.J. Bonvin (2009)
3D-DART: a DNA structure modelling server
Nucl. Acids Res., 37 (Web Server Issue):W235-W239 doi:10.1093/nar/gkp287

WHISCY 1.02 – Predict Protein-protein Interfaces

WHISCY 1.02

:: DESCRIPTION

WHISCY (What information does surface conservation yield?) is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

De Vries SJ, van Dijk ADJ, and Bonvin AMJJ
WHISCY: What information does surface conservation yield? Application to data-driven docking.
Proteins: Struc. Funct. & Bioinformatics; 2006, 63(3): 479-489.

CPORT – Prediction of Protein-protein Interface Residues

CPORT

:: DESCRIPTION

CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
de Vries SJ1, Bonvin AM.

PRODIGY 2.0 – Predicting the Binding Affinity of Protein-protein Complexes

PRODIGY 2.0

:: DESCRIPTION

PRODIGY (PROtein binDIng enerGY prediction) webserver predict of the binding affinity in protein-protein complexes.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 PRODIGY

:: MORE INFORMATION

Citation

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A.
Bioinformatics. 2016 Aug 8. pii: btw514.

HADDOCK 2.2 – Docking approach for the Modeling of Biomolecular Complexes

HADDOCK 2.2

:: DESCRIPTION

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.

Haddock Server

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

  HADDOCK 

:: MORE INFORMATION

Citation

The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes.
van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM.
J Mol Biol. 2015 Sep 24. pii: S0022-2836(15)00537-9. doi: 10.1016/j.jmb.2015.09.014

Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003).
HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.
J. Am. Chem. Soc. 125, 1731-1737

S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.
Proteins: Struc. Funct. & Bioinformatic 69, 726-733 (2007).