Updated manual (#393)

* Update AlphaPulldown_manual.md

---------

Co-authored-by: Konstantin Gilep <82955438+gilep@users.noreply.github.com>
Co-authored-by: Dingquan Yu <44894955+dingquanyu@users.noreply.github.com>

manuals/old_manual.md

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+# AlphaPulldown
+[![Downloads](https://static.pepy.tech/badge/alphapulldown)](https://pepy.tech/project/alphapulldown)  [![python3.10](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/) ![GPL3 license](https://img.shields.io/badge/license-GPLv3-green)
+
+## 🥳 AlphaPulldown has entered the era of version 2.0 (beta version 2.0.0b2)
+We have brought some exciting useful features to AlphaPulldown and updated its computing environment. 
+
+
+AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer:
+* provides a convenient command line interface to screen a bait protein against many candidates, calculate all-versus-all pairwise comparisons, test alternative homo-oligomeric states, and model various parts of a larger complex
+* separates the CPU stages (MSA and template feature generation) from GPU stages (the actual modeling)
+* allows modeling fragments of proteins without recalculation of MSAs and keeping the original full-length residue numbering in the models
+* summarizes the results in a CSV table with AlphaFold scores, pDockQ and mpDockQ, PI-score, and various physical parameters of the interface
+* provides a Jupyter notebook for an interactive analysis of PAE plots and models
+* 🆕 refactorised codes and removed redundancy
+* 🆕 added a new way of integrating experimental models into AlphaFold pipeline using custom multimeric databases
+* 🆕 integrates cross-link mass spec data with AlphaFold predictions via [AlphaLink2](https://github.com/Rappsilber-Laboratory/AlphaLink2/tree/main) models
+
+## Pre-installation
+Check if you have downloaded necessary parameters and databases (e.g. BFD, MGnify etc.) as instructed in [AlphFold's documentation](https://github.com/deepmind/alphafold). You should have a directory like below:
+ ```
+ alphafold_database/                             # Total: ~ 2.2 TB (download: 438 GB)
+    bfd/                                   # ~ 1.7 TB (download: 271.6 GB)
+        # 6 files.
+    mgnify/                                # ~ 64 GB (download: 32.9 GB)
+        mgy_clusters_2018_12.fa
+    params/                                # ~ 3.5 GB (download: 3.5 GB)
+        # 5 CASP14 models,
+        # 5 pTM models,
+        # 5 AlphaFold-Multimer models,
+        # LICENSE,
+        # = 16 files.
+    pdb70/                                 # ~ 56 GB (download: 19.5 GB)
+        # 9 files.
+    pdb_mmcif/                             # ~ 206 GB (download: 46 GB)
+        mmcif_files/
+            # About 180,000 .cif files.
+        obsolete.dat
+    pdb_seqres/                            # ~ 0.2 GB (download: 0.2 GB)
+        pdb_seqres.txt
+    small_bfd/                             # ~ 17 GB (download: 9.6 GB)
+        bfd-first_non_consensus_sequences.fasta
+    uniclust30/                            # ~ 86 GB (download: 24.9 GB)
+        uniclust30_2018_08/
+            # 13 files.
+    uniprot/                               # ~ 98.3 GB (download: 49 GB)
+        uniprot.fasta
+    uniref90/                              # ~ 58 GB (download: 29.7 GB)
+        uniref90.fasta
+ ```
+## Create Anaconda environment
+
+**Firstly**, install [Anaconda](https://www.anaconda.com/) and create AlphaPulldown environment, gathering necessary dependencies 
+```bash
+conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest importlib_metadata hhsuite modelcif
+```
+
+**Optionally**, if you do not have it yet on your system, install [HMMER](http://hmmer.org/documentation.html) from Anaconda
+```bash
+source activate AlphaPulldown
+conda install -c bioconda hmmer
+```
+This usually works, but on some compute systems users may wish to use other versions or optimized builds of already installed HMMER and HH-suite.
+
+## Installation using pip
+
+Activate the AlphaPulldown environment and install AlphaPulldown
+```bash
+source activate AlphaPulldown
+
+python3 -m pip install alphapulldown==1.0.4
+pip install jax==0.4.23 jaxlib==0.4.23+cuda11.cudnn86 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+```
+**For the latest beta version**:
+If you'd like to use AlphaPulldown 2 beta version, feel free to run ```pip install alphapulldown==2.0.0b2``` instead. Please be aware that the beta version
+is actively being updated/fixed. It might not be 100% stable.
+
+**For older versions of AlphaFold**: 
+If you haven't updated your databases according to the requirements of AlphaFold 2.3.0, you can still use AlphaPulldown with your older version of AlphaFold database. Please follow the installation instructions on the [dedicated branch](https://github.com/KosinskiLab/AlphaPulldown/tree/AlphaFold-2.2.0)
+
+## How to develop
+Follow the instructions at [Developing guidelines](./manuals/Developing.md)
+
+------
+
+## Manuals
+AlphaPulldown supports four different modes of massive predictions: 
+
+* ```pulldown``` - to screen a list of "bait" proteins against a list or lists of other proteins
+* ```all_vs_all``` - to model all pairs of a protein list
+* ```homo-oligomer``` - to test alternative oligomeric states
+* ```custom``` - to model any combination of proteins and their fragments, such as a pre-defined list of pairs or fragments of a complex
+
+AlphaPulldown will return models of all interactions, summarize results in a score table, and will provide a [Jupyter](https://jupyter.org/) notebook for an interactive analysis, including PAE plots and 3D displays of models colored by chain and pLDDT score.
+
+## Examples
+
+Example 1 is a case where ```pulldown``` mode is used. Manual: [example_1](./manuals/example_1.md)
+
+Example 2 is a case where ```custom``` and ```homo-oligomer``` modes are used. Manual: [example_2](./manuals/example_2.md) 
+
+Example 3 is demonstrating the usage of multimeric templates for guiding AlphaFold predictions. Manual: [example_3](./manuals/example_3.md) 
+
+```all_vs_all``` mode can be viewed as a special case of the ```pulldown``` mode thus the instructions of this mode are added as Appendix in both manuals mentioned above. 
+
+## Citations
+If you use this package, please cite as the following:
+```python
+@Article{AlphaPUlldown,
+  author  = {Dingquan Yu, Grzegorz Chojnowski, Maria Rosenthal, and Jan Kosinski},
+  journal = {Bioinformatics},
+  title   = {AlphaPulldown—a python package for protein–protein interaction screens using AlphaFold-Multimer},
+  year    = {2023},
+  volume  = {39},
+  issue  = {1},
+  doi     = {https://doi.org/10.1093/bioinformatics/btac749}
+}
+```