From b702f7a63081aeedb49231dfefa38a5d1c56e6b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr> Date: Fri, 26 Apr 2024 15:00:57 +0000 Subject: [PATCH] Update README.md --- README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e0206cb..388aff3 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,16 @@ # WARIO: Weighted fAmilies of contact maps to chaRacterize conformational ensembles of (highly-)flexIble prOteins -WARIO is a tool for the structural characterization of highly-flexible proteins. WARIO takes as input a conformational ensemble (e.g. generated form molecular dynamics simulations or other sampling methods) and represents it as a weighted family of contact maps. Contact is redefined by a continuous function, taking values in $[0,1]$, that incorporates the relative orientation of the interacting residues as well as the sequence information. Then, the featured data is embedded into a 10-dimensional [UMAP](https://umap-learn.readthedocs.io/en/latest/index.html) space and clustered using the [HDBSCAN](https://hdbscan.readthedocs.io/en/latest/#) algorithm. Finally, the average values of the contact function across each cluster conformation are represented as cluster-specific contact maps. The maps are assigned with a weight given by the cluster occupancy. +WARIO is a tool for the structural characterization of highly-flexible proteins. WARIO takes as input a conformational ensemble (e.g. generated form molecular dynamics simulations or other sampling methods) and represents it as a weighted family of contact maps. Contact is redefined by a continuous function, taking values in $[0,1]$, that incorporates the relative orientation of the interacting residues as well as the sequence information. Then, the featured data is embedded into a 10-dimensional [UMAP](https://umap-learn.readthedocs.io/en/latest/index.html) space and clustered using the [HDBSCAN](https://hdbscan.readthedocs.io/en/latest/#) algorithm. Finally, the average values of the contact function across each cluster conformation are represented as cluster-specific contact maps. The maps are assigned with a weight given by the cluster occupancy. The following figure illustrates the main steps of the pipeline. + +<br /> +<br /> +<br /> +<div align="center"> +<img src="pipeline.png" width="800" height="400"> +</div> +<br /> +<br /> +<br /> #### Running WARIO -- GitLab