Tag: Docking

JabberDock – Protein Docking using a density-based descriptor for Atoms Charge and Dynamics

JabberDock

:: DESCRIPTION

JabberDock tackles the problem of protein-protein docking while accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility.

::DEVELOPER

Degiacomi Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

JabberDock

:: MORE INFORMATION

Citation:

Rudden LSP, Degiacomi MT.
Transmembrane Protein Docking with JabberDock.
J Chem Inf Model. 2021 Mar 22;61(3):1493-1499. doi: 10.1021/acs.jcim.0c01315. Epub 2021 Feb 26. PMID: 33635637; PMCID: PMC8041277.

SEED 4.0.0 – Solvation Energy for Exhaustive Docking

SEED 4.0.0

:: DESCRIPTION

SEED is a program for docking libraries of fragments with solvation energy evaluation.The docking approach implemented in the program SEED determines optimal positions and orientations of small-to-medium-sized molecular fragments in the binding site of a rigid protein (hereafter also referred to as receptor) and ranks them according to their binding energy.

::DEVELOPER

Prof. Amedeo Caflisch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SEED

:: MORE INFORMATION

Citation

Majeux N, Scarsi M, Caflisch A
Efficient electrostatic solvation model for protein-fragment docking.
Proteins: Struct. Funct. Genet 42, 256-268, 2001

DockAFM – Docking Structures under an AFM surface

DockAFM

:: DESCRIPTION

DockAFM is an online computational tool for scoring the agreement between 3D atomic structures and experimental envelopes obtained by Atomic Force Microscopy (AFM).

::DEVELOPER

CEA, LIFE SCIENCES DIVISION

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 15;29(24):3230-1. doi: 10.1093/bioinformatics/btt561. Epub 2013 Sep 26.
DockAFM: benchmarking protein structures by docking under AFM topographs.
Chaves RC1, Pellequer JL.

MPRDock – Protein-ensemble-RNA Docking by efficient Consideration of Protein Flexibility

MPRDock

:: DESCRIPTION

The MPRDOCK server is to predict the complex structure between proteins and nucleic acids through ensemble docking of multiple protein structures that are built based by homology modeling.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

He J, Tao H, Huang SY.
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.
Bioinformatics. 2019 Dec 1;35(23):4994-5002. doi: 10.1093/bioinformatics/btz388. PMID: 31086984.

HDOCK 1.1 – Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy

HDOCK 1.1

:: DESCRIPTION

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HDOCK 

:: MORE INFORMATION

Citation:

Yan Y, Zhang D, Zhou P, Li B, Huang SY.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373. doi: 10.1093/nar/gkx407. PMID: 28521030; PMCID: PMC5793843.

pyDockWEB – Rigid-body docking and scoring by pyDock

pyDockWEB

:: DESCRIPTION

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm

::DEVELOPER

Protein Interactions and Docking Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):1698-9. doi: 10.1093/bioinformatics/btt262. Epub 2013 May 9.
pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
Jiménez-García B1, Pons C, Fernández-Recio J.

pyDockSAXS – Protein-protein Interactions using SAXS and Computational Docking

pyDockSAXS

:: DESCRIPTION

pyDockSAXS server is a web server for rigid-body protein-protein docking that combines computational and experimental information.

::DEVELOPER

pyDockSAXS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

pyDockSAXS: protein-protein complex structure by SAXS and computational docking.
Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J.
Nucleic Acids Res. 2015 Apr 20. pii: gkv368.

FlexAID 2.48 / NRGsuite 2.48f – Revisiting Docking on Non-Native-Complex Structures

FlexAID 2.48 / NRGsuite 2.48f

:: DESCRIPTION

NRGsuite is a PyMOL plugin to perform docking simulations in real time using FlexAID.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

NRGsuite

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

 NRGsuite , FlexAID.

:: MORE INFORMATION

Citation

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.
Gaudreault F, Morency LP, Najmanovich RJ.
Bioinformatics. 2015 Aug 6. pii: btv458.

FlexAID: Revisiting Docking on Non-Native-Complex Structures.
Gaudreault F, Najmanovich RJ.
J Chem Inf Model. 2015 Jul 27;55(7):1323-36. doi: 10.1021/acs.jcim.5b00078.

eBoxSize 1.1 – Calculating an optimal box size for Ligand Docking and Virtual Screening

eBoxSize 1.1

:: DESCRIPTION

eBoxSize calculates an optimal box size for a query ligand in order to maximize the accuracy of molecular docking.

::DEVELOPER

Computational Systems Biology Group,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

eBoxSize

:: MORE INFORMATION

Citation

Feinstein WP, Brylinski M.
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.
J Cheminform. 2015 May 15;7:18. doi: 10.1186/s13321-015-0067-5. PMID: 26082804; PMCID: PMC4468813.

MM-ISMSA – Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics

MM-ISMSA

:: DESCRIPTION

MM-ISMSA is an ultrafast and accurate scoring function for protein-protein and protein-ligand docking

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

MM-ISMSA

:: REQUIREMENTS

  • Windows / Linux
  • Python
  • PyMOL

:: DOWNLOAD

  MM-ISMSA

:: MORE INFORMATION

Citation

Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking.
J Chem Theory Comput. 2012 Sep 11;8(9):3395-3408