Merge pull request #68 from volkamerlab/update_READMEs

Update README's

README.md

@@ -27,17 +27,17 @@ This repository holds the following resources:
 
     3.1. Notebooks covering the full analyses regarding the fragment and combinatorial libraries as described in 
           the corresponding paper.  
-    3.2. WIP: Notebooks providing a custom filtering framework to reduce the fragment library size.
+    3.2. Notebooks providing a custom filtering framework to reduce the fragment library size.
 
-Please find detailed description of files in `data/` and `notebooks/` in the folders' `README` files.
+Please find detailed descriptions of files in `data/` and `notebooks/` in the folders' `README` files.
 
 ## Description
 
 **Exploring the kinase inhibitor space using subpocket-focused fragmentation and recombination**
 
 Protein kinases play a crucial role in many cell signaling processes, 
 making them one of the most important families of drug targets.
-Fragment-based drug design has proven useful as one approach to develop novel kinase inhibitors. 
+Fragment-based drug design has proven useful as one approach to developing novel kinase inhibitors. 
 Usually, fragment-based methods follow a knowledge-driven approach, i.e., optimizing a focused set of fragments into 
 molecular hits. 
 
@@ -49,10 +49,10 @@ well as back pocket 1 and 2 (B1 and B2), based on defined pocket-spanning residu
 Each co-crystallized ligand is fragmented using the BRICS algorithm and its fragments are assigned to the respective 
 subpocket they occupy. 
 Following this approach, a fragment library is created with respective subpocket pools. This fragment library enables 
-an in-depth analysis of the chemical space of known kinase inhibitors, and can be used to enumerate recombined 
+an in-depth analysis of the chemical space of known kinase inhibitors and can be used to enumerate recombined 
 fragments in order to generate novel potential inhibitors.
 
-WIP: Custom KinFragLib provides a pipeline to filter the fragments in KinFragLib checking for unwanted substructures (PAINS and Brenk et al.), lead-/drug-likeness (Rule of Three and QED), synthesizability (similarity to buyable building blocks and SYBA) and pairwise retrosynthesizability. Each filter can be (de-)activated and the parameters can be modified by the user to create a customized filtered fragment library. 
+We have added an extension with *CustomKinFragLib* which provides a pipeline to filter the fragments in KinFragLib checking for unwanted substructures (PAINS and Brenk et al.), lead-/drug-likeness (Rule of Three and QED), synthesizability (similarity to buyable building blocks and SYBA) and pairwise retrosynthesizability. Each filter can be (de-)activated and the parameters can be modified by the user to create a customized filtered fragment library. 
 
 ## Quick start
 
@@ -103,7 +103,7 @@ We are looking forward to hearing from you!
 
 ## License
 
-This resource is licensed under the [MIT](https://opensource.org/licenses/MIT) license, a permissive open source license.
+This resource is licensed under the [MIT](https://opensource.org/licenses/MIT) license, a permissive open-source license.
 
 ## Citation
 

data/fragment_library_custom_filtered/README.md

@@ -1,4 +1,4 @@
-# WIP: Custom filtered fragment library
+# Custom filtered fragment library
 
 The (full) fragment library resulting from the KinFragLib fragmentation procedure comprises 7486 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases (see `data/fragment_library/`).
 
@@ -11,5 +11,6 @@ To reduce the fragment library size and enable the recombination avoiding combin
 5. Filter for pairwise retrosynthesizability (using ASKCOS) \[optional\]
 
 - `custom_filter_results.csv`: File containing the filtering results, including per fragment, from the pre-filtered library, the SMILES and subpocket as indices, the calculated scores and boolean columns, if a fragment passes a specific filter, generated by the filtering steps.
+- `AP.sdf`, `FP.sdf`, `GA.sdf`, `SE.sdf`, `B1.sdf`, and `B2.sdf`: custom filtered fragment library organized by subpocket (as decribed in `data/fragment_library`)
 
-Please refer to the notebook `notebooks/custom_kinfraglib/2_1_custom_filters_pipeline.ipynb` to check how the data was generated and/or to generate your own custom fragment library (de-)activating filters and modifying the filtering parameters.
+Please refer to the notebook `notebooks/custom_kinfraglib/2_1_custom_filters_pipeline.ipynb` to check how the data was generated and/or to generate your own custom fragment library (de-)activating filters and modifying the filtering parameters.