From 15a6f8bb751fa8480e9df6995755f9039cbed7e8 Mon Sep 17 00:00:00 2001 From: Paula Kramer Date: Mon, 6 May 2024 17:50:19 +0200 Subject: [PATCH] add custom in main readme --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 205ea642..fc6c08ba 100644 --- a/README.md +++ b/README.md @@ -27,9 +27,9 @@ 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 @@ -37,7 +37,7 @@ Please find detailed description of files in `data/` and `notebooks/` in the fol 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