Tag: Docking

MGA-Glide 1.0 – Grid-based Protein-ligand Docking software

MGA-Glide 1.0

:: DESCRIPTION

MGA-Glide is a novel deep conformational search method for grid-based protein-ligand docking software.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MGA-Glide

:: MORE INFORMATION

Citation

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem.
Ban T, Ohue M, Akiyama Y.
Comput Biol Chem. 2018 Apr;73:139-146. doi: 10.1016/j.compbiolchem.2018.02.008.

PPDbench – Benchmarking of Docking software on Protein-peptide Complexes

PPDbench

:: DESCRIPTION

PPDbench server is made in order to provide an easy webserver to calculate FNAT, L-RMSD and I-RMSD values of docked and original poses of protein-peptide complexe’s.

::DEVELOPER

PPDbench team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Benchmarking of different molecular docking methods for protein-peptide docking.
Agrawal P, Singh H, Srivastava HK, Singh S, Kishore G, Raghava GPS.
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):426. doi: 10.1186/s12859-018-2449-y.

KiDoQ – Prediction of Dihydrodipicolinate synthase inhibtors using Docking and QSAR

KiDoQ

:: DESCRIPTION

KiDoQ, a web server has been developed to serve scientific community working in the field of designing inhibitors against Dihydrodipicolinate synthase (DHDPS), a potential drug target enzyme of a unique bacterial DAP/Lysine pathway.

::DEVELOPER

KiDoQ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 11;11:125. doi: 10.1186/1471-2105-11-125.
KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials.
Garg A1, Tewari R, Raghava GP.

Sculptor 2.1.1 – Docking & Visualization for Atomic Structures

Sculptor 2.1.1

:: DESCRIPTION

Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment.

::DEVELOPER

biomachina.org

:: SCREENSHOTS

:: REQUIREMENTS

  • Window / Linux / Mac OsX

:: DOWNLOAD

Sculptor

:: MORE INFORMATION

Citation

Stefan Birmanns, Mirabela Rusu, and Willy Wriggers.
Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes.
J. Struct. Biol., Vol. 173, pp. 428–435, 2011.

MolFit 2 – Protein-Protein docking Program

MolFit 2

:: DESCRIPTION

MolFit represents each molecule via a 3-dimensional grid of complex numbers and estimates the extent of geometric and chemical surface complementarity by correlating the grids

::DEVELOPER

MolFit Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MolFit

:: MORE INFORMATION

Citation

Proteins. 2005 Aug 1;60(2):195-201.
Docking to single-domain and multiple-domain proteins: old and new challenges.
Ben-Zeev E, Kowalsman N, Ben-Shimon A, Segal D, Atarot T, Noivirt O, Shay T, Eisenstein M.

VcPpt – Protein Ligend Docking & in silico High-throughput Screening

VcPpt

:: DESCRIPTION

VcPpt is an independently developed extension for Vina, a program for flexible ligand docking under Windows OS.Carry out high-throughput screening of compound libraries with Vina and cluster resulting PDB files of ligands by binding energies and by binding positions. Results processing functions do not require Vina installed. Screening scale is unlimited.

::DEVELOPER

BiochemLabSolutions.com

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 VcPpt

:: MORE INFORMATION