• Chimera

  • Referenced in 20 articles [sw10908]
  • including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality...
  • AutoDock

  • Referenced in 9 articles [sw09659]
  • AutoDock is a suite of automated docking tools. It is designed to predict how small ... main programs: autodock performs the docking of the ligand to a set of grids describing ... grids. In addition to using them for docking, the atomic affinity grids can be visualised...
  • ARVO

  • Referenced in 14 articles [sw00049]
  • proteins, hydration effects, drug binding, molecular docking, etc., it is important to have efficient...
  • DOCK

  • Referenced in 5 articles [sw07835]
  • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. n this paper ... describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated ... into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction ... flexibility. For all testcases, at least one docked position is generated within...
  • PacthDock

  • Referenced in 4 articles [sw12399]
  • PatchDock is an algorithm for molecular docking. The input is two molecules of any type ... image segmentation techniques used in Computer Vision. Docking can be compared to assembling a jigsaw...
  • Situs

  • Referenced in 3 articles [sw09515]
  • Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy. Three ... package of routines. The precision of the docking has allowed for the extraction of unique...
  • ZDOCK

  • Referenced in 3 articles [sw12737]
  • Protein Docking. ZDOCK: Performs a full rigid-body search of docking orientations between two proteins...
  • ADP_EM

  • Referenced in 3 articles [sw16893]
  • fast exhaustive multi-resolution docking for high-throughput coverage. Motivation: Efficient fitting tools are needed ... novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density...
  • HexServer

  • Referenced in 2 articles [sw21768]
  • HexServer: an FFT-based protein docking server powered by graphics processors. HexServer (http://hexserver.loria.fr ... first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using ... graphics processors simultaneously, a typical 6D docking run takes approximately 15 s, which ... magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions...
  • Macrodox

  • Referenced in 2 articles [sw08087]
  • calculating the rate of attainment of optimum docking conformations of protein-protein, protein ... generate a representative search of plausible docked complexes using a Brownian dynamics algorithm and make ... allow an automated force-guided search of docked conformers which would avoid trapping in local ... bimolecular diffusive rate constant of attainment of docked complexes by Brownian dynamics...
  • BiGGER

  • Referenced in 2 articles [sw10909]
  • Applying constraint programming to rigid body protein docking. In this paper we show how Constraint ... BiGGER some efficiency advantages over popular protein docking methods that use Fourier transforms to match ... between points of the two structures to dock, which allows the use of experimental data ... programming provides a different approach to protein docking (and fitting of shapes in general) that...
  • AutoDock Vina

  • Referenced in 4 articles [sw09661]
  • open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg...
  • F2Dock

  • Referenced in 2 articles [sw12735]
  • F2Dock, a rigid-body protein-protein docking software, have been implemented in a client-server ... corresponding publications, refer to the Protein-protein docking project page...
  • ConsDock

  • Referenced in 1 article [sw09660]
  • macromolecular target of interest. Because of docking and scoring limitations, it is more difficult ... present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely ... used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated ... several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses...
  • PDB_Hydro

  • Referenced in 3 articles [sw14705]
  • water between ligands and receptors in docking simulations...
  • DeepVS

  • Referenced in 1 article [sw16458]
  • Boosting Docking-based Virtual Screening with Deep Learning. In this work, we propose a deep ... learning approach to improve docking-based virtual screening. The introduced deep neural network, DeepVS, uses ... output of a docking program and learns how to extract relevant features from basic data ... Decoys (DUD), using the output of two docking programs: AutodockVina1.1.2 and Dock6.6. Using a strict...
  • CGV

  • Referenced in 2 articles [sw19315]
  • dynamically with the help of a flexible docking framework. Several novel techniques, including enhanced dynamic...
  • GANM

  • Referenced in 1 article [sw08551]
  • GANM: A protein-ligand docking approach based on genetic algorithm and normal modes. We describe ... analysis in order to achieve protein-ligand docking simulations that take into account global...
  • Ribosome Builder

  • Referenced in 1 article [sw10930]
  • long time-scale events, such as docking of translation factors and mRNA translocation. An embedded ... project include simulation of tetraloop folding, docking of an mRNA on the 30S subunit...
  • AMMOS_ProtLig

  • Referenced in 1 article [sw06613]
  • automatically processes the output files after post-docking optimization with AMMOS_ProtLig. The module retrieves...