Enhancing Protein-Drug Binding Prediction

Combining molecular simulation and eScience technologies

Image: Drug binding to receptor protein by Sam Hertig – http://www.samhertig.ch/blog/wp-content/uploads/2015/10/m4v1m2.jpg

Drugs typically exert their effects by interactions with and binding to proteins. Accurate methods are therefore needed to evaluate protein-drug binding and interaction. However, predicting their binding in an accurate way is typically difficult and computationally demanding. In this ASDI project we developed and implemented smart algorithms to accurately and automatically parameterize interactions involving a drug compound of interest, and we combined molecular dynamics (MD) simulation together with other computational approaches needed for protein-drug binding evaluation. By integrating these in the novel microservice-driven MDStudio platform and by developing a dedicated microservice to allow parallel execution of MD at heterogeneous (super)computing facilities, we have enabled and greatly facilitated efficient execution of complex MD-based workflows for protein-binding prediction. The platform, tools and algorithms developed during this project have been made available as open access software.

Participating organisations

Vrije Universiteit Amsterdam
CWI
Netherlands eScience Center
Life Sciences
Life Sciences
Natural Sciences & Engineering
Natural Sciences & Engineering

Impact

Output

Team

DG
Daan Geerke
Principal investigator
VU University Amsterdam
Lourens Veen
eScience Research Engineer
Netherlands eScience Center
MvD
Marc van Dijk
Postdoctoral researcher
Vrije Universiteit Amsterdam
ME
Martin Engler
Postdoctoral reseacher
Centrum Wiskunde en Informatica
AM
Lars Ridder
Lars Ridder
eScience Coordinator
Netherlands eScience Center
Felipe Zapata
Felipe Zapata
eScience Research Engineer
Netherlands eScience Center
Rena Bakhshi
eScience Research Engineer
Netherlands eScience Center

Related projects

FEDMix

Fusible evolutionary deep neural network mixture learning from distributed data for robust medical...

Updated 20 months ago
Finished

Integrated omics analysis for small molecule-mediated host-microbiome interactions

Advancing our understanding of molecular mechanisms of health and disease

Updated 24 months ago
Finished

DeepRank

Scoring 3D protein-protein interaction models using deep learning

Updated 20 months ago
Finished

Googling the cancer genome

Identification and prioritization of cancer-causing structural variations in whole genomes

Updated 1 week ago
Finished

3D Printing of human body parts

Deep learning algorithms for more accurate implants

Updated 20 months ago
Finished

Data quality in a distributed learning environment

Vast amounts of data to improve cancer treatment decisions

Updated 24 months ago
Finished

Massive Biological Data Clustering, Reporting and Visualization Tools

Sequence validation in the DNA barcoding project

Updated 20 months ago
Finished

Computational Chemistry Made Easy

Bringing concepts from distributed computing and bioinformatics to the field of computational...

Updated 20 months ago
Finished

Chemical Analytics Platform

Managing and exploiting growing data resources in chemical design

Updated 20 months ago
Finished

Related software

Cerise

CE

Cerise is a service for running CWL workflows on HPC resources. You add software, tool descriptions, and connection information, then your user runs workflows whenever they want.

Updated 6 months ago
1

cerulean

CE

A Python 3 library for talking to HPC clusters and supercomputers.

Updated 29 months ago
1

MDStudio

MD

A tool to run molecular dynamics workflows.

Updated 14 months ago
10 4

yatiml

YA

Python library for YAML type inference, schema checking and syntactic sugar.

Updated 29 months ago
1