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iScore: A novel graph kernel-based function for scoring protein-protein docking models [article]

Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M.J.J. Bonvin, Li C. Xue
2018 bioRxiv   pre-print
Here we present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms with a score obtained using a graph representation of the protein-protein interfaces and a measure  ...  This work represents the first successful demonstration of graph kernel to protein interfaces for effective discrimination of near-native and non-native conformations of protein complexes.  ...  ACKNOWLEDGEMENTS Walter from Utrecht University for helpful discussions. The content is solely the responsibility of the authors and does not necessarily represent the official views of the sponsors.  ... 
doi:10.1101/498584 fatcat:wwt674vqjnfpdhygedlv3vwz5y

iScore: A novel graph kernel-based function for scoring protein-protein docking models

Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue, Alfonso Valencia
2019 Bioinformatics  
Here we present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms with a score obtained using a graph representation of the protein-protein interfaces and a measure  ...  This work represents the first successful demonstration of graph kernels to protein interfaces for effective discrimination of near-native and non-native conformations of protein complexes.  ...  Discussion We have developed a novel graph-kernel based scoring function, iScore, for scoring and ranking docking models of protein-protein complexes.  ... 
doi:10.1093/bioinformatics/btz496 pmid:31199455 pmcid:PMC6956772 fatcat:jejx6kx7xjanhpoakh5sunmsi4

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines [article]

Nicolas Renaud, Yong Jung, Vasant Honavar, Cunliang Geng, Alexandre Bonvin, Li Xue
2019 bioRxiv   pre-print
We recently published iScore, a novel graph kernel based scoring function. iScore ranks docking models based on their interface graph similarities to the training interface graph set. iScore uses a support  ...  Computational docking is a promising tool to model three-dimensional (3D) structures of protein-protein complexes, which provides fundamental insights of protein functions in the cellular life.  ...  Zou, An iterative knowledge-based scoring function for 351 protein-protein recognition, Proteins: Structure, Function, and Bioin-352 formatics 72 (2) (2008) 557-579. The method is based as input.  ... 
doi:10.1101/788166 fatcat:c5l7fiivp5debfp4xnznznkygy

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

Nicolas Renaud, Yong Jung, Vasant Honavar, Cunliang Geng, Alexandre M.J.J. Bonvin, Li C. Xue
2020 SoftwareX  
We recently published iScore, a novel graph kernel based scoring function. iScore ranks docking models based on their interface graph similarities to the training interface graph set. iScore uses a support  ...  Computational docking is a promising tool to model three-dimensional (3D) structures of protein-protein complexes, which provides fundamental insights of protein functions in the cellular life.  ...  ACI 1640834) and the National Institutes of Health (NCATS UL1 TR002014-01), the Center for Big Data Analytics and Discovery Informatics which is cosponsored by the Institute for Cyberscience, USA, the  ... 
doi:10.1016/j.softx.2020.100462 pmid:35419466 pmcid:PMC9005067 fatcat:qbxbq627wjdilf4vzhdza3auuy

DeepRank: A deep learning framework for data mining 3D protein-protein interfaces [article]

Nicolas Renaud, Cunliang Geng, Sonja Georgievska, Francesco Ambrosetti, Lars Ridder, Dario F. Marzella, Alexandre M.J.J. Bonvin, Li C. Xue
2021 bioRxiv   pre-print
We demonstrate the performance of DeepRank on two distinct challenges: The classification of biological versus crystallographic PPIs, and the ranking of docking models.  ...  The vast amount of experimentally and computationally resolved protein-protein interfaces (PPIs) offers the possibility of training deep learning models to aid the predictions of their biological relevance  ...  We compared DeepRank with two leading scoring functions, the HADDOCK scoring function and the recently developed iScore 39,40 , a graph-kernel based scoring function.  ... 
doi:10.1101/2021.01.29.425727 fatcat:nubuph4jlveftohrx3v2c2q3ci

Native or non-native protein-protein docking models? Molecular dynamics to the rescue [article]

Zuzana Jandova, Attilio Vittorio Vargiu, Alexandre M.J.J. Bonvin
2021 bioRxiv   pre-print
We assessed here if a protocol based on molecular dynamics (MD) simulations would allow to distinguish native from non-native models to complement scoring functions used in docking.  ...  Molecular docking excels at creating a plethora of potential models of protein-protein complexes.  ...  Francesco Ambrosetti for his input on machine learning.  ... 
doi:10.1101/2021.04.02.438171 fatcat:rmnpnr7qavcuvcgxtbswiw3h5q

Graph Representation Learning in Biomedicine [article]

Michelle M. Li, Kexin Huang, Marinka Zitnik
2021 arXiv   pre-print
With the remarkable success of representation learning in providing powerful predictions and insights, we have witnessed a rapid expansion of representation learning techniques into modeling, analyzing  ...  We synthesize a spectrum of algorithmic approaches that, at their core, leverage graph topology to embed networks into compact vector spaces, and capture the breadth of ways in which representation learning  ...  M.M.L. is supported by T HG from the National Human Genome Research Institute and a National Science Foundation Graduate Research Fellowship.  ... 
arXiv:2104.04883v2 fatcat:7raztbocfngm3pv57l2iwadgre

BioExcel-2 Deliverable 2.3 - Progress report and update on training and dissemination plan

Marta Lloret-Llinares, Vera Matser, Michelle Mendonca, Peter Meadley
2020 Zenodo  
For each course, we present the con [...]  ...  We also present the future strategy for dissemination and updated plans for training activities in the second half of the project.  ...  Xue iScore: A novel graph kernel-based function for scoring protein-protein docking models Bioinformatic s http://dx.do i.org/10.10 93/bioinfor matics/btz4 96 http://dx.doi.org/10 .1093  ... 
doi:10.5281/zenodo.4604924 fatcat:iug6ufyrxnb75ndcsv37n77eoe