° | Building a protein model |
This macro builds a protein model using a FASTA sequence of the target, and optionally template structures and alignments. AI-based ab initio structure predictions are made locally using ESMFold and OmegaFold (7 GB of disk space needed). If 'foldmethod' is set to 'All', AlphaFold predictions will also be used (75 GB of disk space needed). Written by: Elmar Krieger License: GNU GPL Last modified: 2025/09/12
° | Docking a ligand to a receptor |
This macro runs VINA or AutoDock to predict the structure of a ligand-receptor complex. It can also continue a docking run that got interrupted. An analysis log file is written at the end. Written by: Elmar Krieger License: GNU GPL Last modified: 2025/09/08
° | Docking many ligands to a receptor to perform virtual screening |
This macro runs VINA or AutoDock to dock multiple ligands against a receptor and saves a sorted table of their binding energies, as well as the corresponding complexes Written by: Elmar Krieger License: GNU GPL Last modified: 2025/06/28
° | Docking a ligand to a receptor ensemble with flexible side-chains |
This macro runs VINA or AutoDock to predict the structure of a ligand-receptor complex. Receptor flexibility is considered by creating a receptor ensemble with alternative high-scoring solutions of the side-chain rotamer network. An analysis log file is written at the end. The macro can also continue a docking run that got interrupted, especially if the scene has not been moved or rotated manually during the docking. Written by: Elmar Krieger License: GNU GPL Last modified: 2025/06/07
° | Showing the docking results interactively |
This macro provides an interactive player to cycle through the docking poses and clusters Written by: Elmar Krieger License: GNU GPL Last modified: 2025/04/28
° | Rescore ligand poses with an energy minimization and local docking |
This macro loads a receptor-ligand complex obtained with YASARA's own docking macros or other software, energy-minimizes each ligand pose and rescores it using AutoDock VINA's local search, confined closely to the original ligand pose. Written by: Elmar Krieger License: GNU GPL Last modified: 2024/11/07
° | Docking a ligand to a receptor locally |
This macro runs VINA or AutoDock to sample local ligand conformations in a user-supplied complex. An analysis log file is written at the end. Written by: Elmar Krieger License: GNU GPL Last modified: 2024/09/18
° | Docking a covalently bound ligand to a receptor |
This macro runs VINA or AutoDock to predict the structure of a covalent ligand-receptor complex. It can also continue a docking run that got interrupted. An analysis log file is written at the end. Written by: Elmar Krieger License: GNU GPL Last modified: 2024/09/18
° | Building a homology model quickly |
This macro builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments. It takes some shortcuts (alignment quality, number of templates, refinement) to finish as quickly as possible Written by: Elmar Krieger License: GNU GPL Last modified: 2024/04/10
° | Building a homology model |
This macro builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments. To include AI-based ab initio structure prediction, use the 'pm_build' macro. Written by: Elmar Krieger License: GNU GPL Last modified: 2024/04/10
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