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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
vector machine approach with random-walk graph kernels to classify and rank protein-protein interfaces.  ...  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  ...  As a whole, the software provides 296 a user friendly solution for ranking PPIs more efficiently and accurately. 290 on a support vector machine classification using random-walk graph kernels 291  ... 
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  
vector machine approach with random-walk graph kernels to classify and rank protein-protein interfaces.  ...  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  ...  LX acknowledges financial support from the Netherlands Organisation for Scientific Research (Veni grant 722.014.005) and from an Accelerating Scientific Discovery (ASDI) grant from the Netherlands eScience  ... 
doi:10.1016/j.softx.2020.100462 pmid:35419466 pmcid:PMC9005067 fatcat:qbxbq627wjdilf4vzhdza3auuy

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  
set generated by a wide variety of docking approaches (i.e. docking software-non-specific). iScore ranks among the top scoring approaches on the CAPRI score set (13 targets) when compared with the 37  ...  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  ...  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