Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
CAP - Catabolite gene Activating Protein (1BER)
DNA - GATTACAGATTACAGATTACA Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI) DNA - GATTACAGATTACAGATTACA TBP - TATA box  Binding Protein (1C9B)
CAP - Catabolite gene Activating Protein (1BER)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
TBP - TATA box  Binding Protein (1C9B)

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Structure prediction

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Macros

Macros are written using the Yanaconda language. If you already know a programming language, you can learn Yanaconda in 15 minutes, otherwise it may take 30.

To install, just save the macro in the directory yasara/mcr or wherever you want it. The syntax of Yanaconda is described in the YASARA documentation.

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Docking a ligand to a receptor

This macro predicts 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: 2017/07/16

Download: dock_run.mcr

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Docking a ligand to a receptor ensemble with flexible side-chains

This macro predicts 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: 2017/07/03

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Docking a ligand to a receptor locally

This macro samples 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: 2017/05/27

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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: 2017/05/19

Download: dock_play.mcr

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Docking many ligands to a receptor to perform virtual screening

This macro docks 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: 2017/03/24

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Building a homology model

This macro builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2017/03/21

Download: hm_build.mcr

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Building a homology model

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: 2016/12/27