diff --git a/README.md b/README.md index 46ec393..fcf818b 100644 --- a/README.md +++ b/README.md @@ -149,7 +149,7 @@ - uptake type, - sequence. -
+

2. Natural CPPs

@@ -173,6 +173,8 @@ Represents a balanced dataset of CPPs and non-CPPs; often used for model benchmarking. +
+

3. Non-CPPs

Contains negative CPP samples in .txt format. @@ -186,6 +188,8 @@ Contains non-CPP sequences shown not to demonstrate activity experimentally. +
+

4. Non-Natural CPPs

Contains CPPs consisting of non-natural amino acids. @@ -199,6 +203,7 @@ Contains a list of abbreviations for modified amino acids in .txt format (ABBREVIATION: NAME; ...: ...). +---

Useful tools :bookmark_tabs:

@@ -214,6 +219,8 @@ drawing +
+

Modelling of interaction with membrane

For CPPs from 7 to 24 amino acids you can use [PMIpred neural network model](https://pmipred.fkt.physik.tu-dortmund.de/curvature-sensing-peptide/) trained on Molecular Dynamics (MD) data to predict its interaction with the cellular membrane. Please use modelling on neutral membrane for better differentiation between CPPs and non-CPPs. @@ -228,6 +235,8 @@ drawing +
+

Membrane permeability prediction

For so-called stapled peptides consisting of both natural and modified amino acids you can predict membrane permeability using [STAPEP package](https://github.com/dahuilangda/stapep_package) offering the full pipeline from data preprocessing to ML model development and use on novel samples.