Haddock3 online user manual

software/haddock3/index.md

@@ -14,7 +14,7 @@ image:
 
 ![Structure + Binformatic/Biophysical Data => Complex](/images/HADDOCK3-logo.png)  
 
-_Version:_ 3.0 (first release May 2020)  
+_Version:_ 3.0.0 (first alpha release May 2020)  
 
 _Authors:_ Computational structural biology group, Utrecht University  
 
@@ -33,6 +33,22 @@ Fax: +31-30-2537623
 **ATTENTION: This new version is under heavy development and will change abruptly and without warning.**
 
 
+* * *
+
+**HADDOCK3 manual**: [https://www.bonvinlab.org/software/haddock2.4/manual/index.md](/software/haddock2.4/manual.md)
+
+**HADDOCK3 web application**:  The haddock3 web application is still under development. [https://github.com/i-VRESSE/haddock3-webapp](https://github.com/i-VRESSE/haddock3-webapp)
+
+**HADDOCK3 web service**:  -- Not yet available --
+
+**Getting the software**:  [https://www.bonvinlab.org/software/haddock3/](https://www.bonvinlab.org/software/haddock3/)
+
+**Questions about HADDOCK or looking for support?**  [Ask BioExcel](https://ask.bioexcel.eu)
+
+**Questions about code related issue?**  [GitHub issues](https://github.com/haddocking/haddock3/issues)
+
+[**HADDOCK best practice guide**](/software/bpg) - A must read when starting to use our software!
+
 * * *
 
 ## Description

software/haddock3/manual.md

@@ -0,0 +1,101 @@
+---
+layout: page
+title: "HADDOCK3 manual"
+tags: [Jekyll, HADDOCK, Bonvin, Docking, Simulation, Molecular Dynamics, Structural Biology, Computational Biology, Modelling, Protein Structure]
+modified: 2024-06-26T12:34:56.789012-04:00
+comments: false
+title: HADDOCK3 manual
+image:
+  feature: pages/banner_software.jpg
+---
+
+
+# Haddock3 User Manual
+
+Welcome to the haddock3 user manual
+
+
+### Introduction
+
+* [HADDOCK - High Ambiguity Docking](/software/haddock3/manual/haddocking)
+* [Haddock3 modularity](/software/haddock3/manual/haddock3)
+
+
+### [Installation](/software/haddock3/manual/install)
+
+* [Obtaining HADDOCK](/software/haddock3/manual/install#download-haddock3)
+* [CNS](/software/haddock3/manual/install#install-cns)
+* [Virtual environments (conda / venv)](/software/haddock3/manual/install#virtual-environments)
+
+
+### Command Line Interfaces
+
+* [Command Line Interfaces](/software/haddock3/manual/clis)
+
+
+### Preparing input files
+
+* [Haddock3 requirements](/software/haddock3/manual/structure_requirements)
+* [Tools to manipulate structures](/software/haddock3/manual/pdbtools)
+
+
+###  Generating restraints for HADDOCK
+
+* [General introduction](/software/haddock3/manual/intro_restraints)
+* [haddock3-restraints](/software/haddock3/manual/restraints_cli)
+* [Symmetry restraints](/software/haddock3/manual/symmetry_restraints)
+* [Ab-initio docking mode](/software/haddock3/manual/abinitio_docking)
+* [Flexibility](/software/haddock3/manual/flexibility)
+
+
+### Generating a docking protocol
+
+* [Configuration file](/software/haddock3/manual/config_file)
+* [Global parameters](/software/haddock3/manual/global_parameters)
+* [Concept of modules / parameters](/software/haddock3/manual/modules_parameters)
+* [Notable parameters](/software/haddock3/manual/important_parameters)
+
+
+### Available modules
+
+* [Module available in haddock3](/software/haddock3/manual/modules.md)
+* [Topology](/software/haddock3/manual/modules/topology)
+* [Sampling](/software/haddock3/manual/modules/sampling)
+* [Refinements](/software/haddock3/manual/modules/refinements)
+* [Scoring](/software/haddock3/manual/modules/scoring)
+* [Analysis](/software/haddock3/manual/modules/analysis)
+
+
+### Docking scenario examples
+
+* [Docking scenarios](/software/haddock3/manual/modules/docking_scenarios)
+* [protein-protein docking]()
+* [antibody-antigen docking]()
+* [protein-ligand docking]()
+* [protein-glycan docking]()
+
+
+### Getting support / How to ask for help
+
+* [Getting support / How to ask for help](/software/haddock3/manual/info)
+* [FAQ](/software/haddock3/faq)
+
+
+### Tutorials
+
+* [Access to various tutorials](/software/haddock3/manual/tutorials)
+* [HADDOCK best practice guide](/software/bpg) - A must read when starting to use our software!
+
+
+### [Online lectures](https://www.youtube.com/user/WeNMRchannel)
+
+
+### Citing haddock3
+
+* [Citing haddock3](/software/haddock3/manual/citing)
+* [Haddck3-related publications](/software/haddock3/manual/publications)
+
+
+### Acknowledgements
+
+* [Acknowledgements](/software/haddock3/manual/acknowledgements)

software/haddock3/manual/abinitio_docking.md

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+---
+layout: page
+title: ""
+excerpt: ""
+tags: [HADDOCK, HADDOCK3, installation, preparation, proteins, docking, analysis, workflows, manual, usage]
+image:
+  feature: pages/banner_software.jpg
+---
+
+* table of contents
+{:toc}
+
+<hr>
+
+# Ab-initio / naive docking protocols
+
+While HADDOCK is ment to use information from coming from experiments, literature or bioinformatic predictions to guide the sampling during the docking, sometimes you cannot obtain such kind of data.
+For this reasons, dedicated parameters can be turned **on** to perform *ab-inito* docking.
+
+Three different ways of doing *ab-inito* docking in haddock3 are discussed below.
+
+
+### Prior considerations
+
+- As ab-initio docking contains very loose information on how the various chains involed should interact, we strongly advise to increase the sampling at `[rigidbody]` docking stage (using `sampling` parameter) as finind a good solution relies on trials and errors.
+- The next trhee *ab-inito* docking solution described below are incompatible with each other, and you should not turn **on** multiple of them at the same time.
+
+
+## Center of mass restraints
+
+Turning **on** the center of mass restraints parameter (`cmrest = true`), will automatically generates restraints between the center of masses of the different chains present the system, and use those during the docking.
+
+This parameter goes together with the `cmtight` paraemter, which controls how the upper limit distance is defined for the center of mass restraints between molecules.
+Each molecule is oriented along its principle components and the x, y and z dimensions are calculated.
+If `cmtight=true`, the molecule distance (size) is set to the average of its smallest two half dimensions.
+If `cmtight=false`, the molecule distance (size) is set to the average of its three half dimensions.
+In case of DNA, RNA, small ligands or glycans, the molecule distance (size) is set to 0.
+The effective upper distance limit for the center of mass distance restraint is the sum of the two molecule distances.
+
+`cmrest` and `cmtight` parameters are accessible in `[rigidbody]` and `[flexref]` modules.
+
+This parameter goes together with its force constant (`kcm`), that can be tuned as well.
+
+Please note that setting `cmrest = true` is more suited for globular structures.
+As for example, for a long bDNA structure, the restraint will be defined to the center of the DNA.
+
+
+## Random Ambiguous Restraints
+
+An other solution is to generate random ambiguous restraints.
+This is performed by turning **on** the `ranair` parameter (`ranair = true`) in the `[rigidbody]` module.
+
+By doing so, for each rigidbody sampling performed, residues on the surface of each chains will be randomly picked together with surrounding ones to define a patch.
+Ambiguous restraints will then be generated between all the patches and rigidbody minimisation performed.
+
+We suggest to turn on `contactairs = true` parameters in later stages of the workflow for CNS modules (`[flexref]`, `[emref]`, `[mdref]`).
+
+
+## Surface restraints
+
+An alternative solution is to turn **on** the `surfrest` parameter (`surfrest = true`).
+By doing so, surface residues are first detected and contact restraints between molecules are generated on the fly.
+These are defined as an ambiguous distance restraint between all backbone (CA, BB or N1) atoms of two molecules (for small ligands all atoms are considered).
+If less than 3 CA and P atoms are found, all atoms will be selected instead.
+The upper limit is set to 7A (or 4.5A in case of small ligands).
+
+Such restraints can be useful in multi-body (N>2) docking to ensure that all molecules are in contact and thus promote compactness of the docking solutions.
+As for the [random AIRs](#random-ambiguous-restraints), surface contact restraints can be used in ab-initio docking; in such a case it is important to have enough sampling of the random starting orientations and this significantly increases the number of structures for rigid-body docking.
+
+Note that this option is computationally more expensive than the [center of mass restraints](#center-of-mass-restraints) and [random AIRs](#random-ambiguous-restraints), as the number of restraints is increasing by the power of the number of resiudes present in the system.
+Also, because of the high number of restraints, the physico-chemical components of the scoring function can be masked by the noise of the AIRs component.
+Therefore setting the weight of the AIR component to 0 (`w_air = 0`), could help the scoring function to better decipher between model conformations.
+
+This parameter goes along with its force constant `ksurf`, that can be tuned.

software/haddock3/manual/acknowledgements.md

@@ -0,0 +1,41 @@
+---
+layout: page
+title: ""
+excerpt: ""
+tags: [HADDOCK, HADDOCK3, installation, preparation, proteins, docking, analysis, workflows, manual, usage]
+image:
+  feature: pages/banner_software.jpg
+---
+
+* table of contents
+{:toc}
+
+<hr>
+
+# Acknowledgements
+
+## Fundings
+
+The development of Haddock3 is made possible thanks to the financial support from Horizon 2020, projects [BioExcel](https://www.bioexcel.eu) [823830](https://cordis.europa.eu/project/id/823830) and [101093290](https://cordis.europa.eu/project/id/101093290), EGI-ACE [101017567](https://cordis.europa.eu/project/id/101017567), and from the Netherlands e-Science Center (027.020.G13), that provided and still provides substancial fundings for software development.
+This allows the HADDOCK team to ensure software quality, imporvements, maintenance and user supports.
+
+
+## User driven developments
+
+In Haddock3, not only we try to provide a powerfull docking tool that can handle a variety of biomolecular entities, but we are also develloping new modules and functionalities based on user requests.
+On a yearly basis, we ask users to fill a survey, allowing us to focus on several different directions to improve the tool and make it more suitable for the community.
+Feature requests can also be performed directly from our [GitHub repository issues](https://github.com/haddocking/haddock3/issues/new/choose).
+
+
+## 20 years of HADDOCK
+
+Haddock3 is the newest version of HADDOCK, an original idea initially developped by [Dominguez, C., Boelens, R. & Bonvin, A. M. J. J. in 2003](https://pubs.acs.org/doi/10.1021/ja026939x).
+Since more than 20 years now, HADDOCK has been improved, going from its first description to several milestones, namely Haddock2.2, Haddock2.4 and now Haddock3.
+
+In november 2023, we celebrated the 20 years anniversary of HADDOCK, where most of the incredible scientists that contributed to its developement attended.
+
+<figure style="text-align: center;">
+<img width="75%" src="20yearshaddock.png" alt="photo 20 years haddock3">
+</figure>
+
+We wish to thank all the students, PhD candidates, PostDoctoral researchers for each of their contribution to the tool, as it allowed to continuously develop new methods and improve HADDOCK functionalities over the years.

software/haddock3/manual/base.md

@@ -0,0 +1,15 @@
+---
+layout: page
+title: ""
+excerpt: ""
+tags: [HADDOCK, HADDOCK3, installation, preparation, proteins, docking, analysis, workflows, manual, usage]
+image:
+  feature: pages/banner_software.jpg
+---
+
+* table of contents
+{:toc}
+
+<hr>
+
+# Name

software/haddock3/manual/citing.md

@@ -0,0 +1,15 @@
+---
+layout: page
+title: ""
+excerpt: ""
+tags: [HADDOCK, HADDOCK3, installation, preparation, proteins, docking, analysis, workflows, manual, usage]
+image:
+  feature: pages/banner_software.jpg
+---
+
+* table of contents
+{:toc}
+
+<hr>
+
+# Name