Benchmarks¶
Rosetta benchmarks
Existing approaches¶
Sequence only¶
intogen
- https://www.intogen.org/search
- oncoDRIVE
- oncoROLE
- http://bg.upf.edu/group/index.php
mCSM: predicting the effects of mutations in proteins using graph-based signatures.
- http://www.ncbi.nlm.nih.gov/pubmed/24281696
- “To understand the roles of mutations in disease, we have evaluated their impacts not only on protein stability but also on protein-protein and protein-nucleic acid interactions”.
- cite{pires_mcsm_2014}
Sequence and structure¶
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
- http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004276
- “The core of the SAAMBE method is a modified molecular mechanics Poisson-Boltzmann Surface Area (MM/PBSA) method with residue specific dielectric constant”.
- cite{petukh_predicting_2015}
MAESTRO cite{laimer_maestro_2015}
- https://biwww.che.sbg.ac.at/?page_id=477
- MAESTRO implements a multi-agent machine learning system.
- Structure based tools AUTO-MUTE [7], CUPSAT [8], Dmutant [9], FoldX [10], Eris [11], PoPMuSiC [12], SDM [13] or mCSM [14] usually perform better than the sequence based counterparts. Recently, SDM and mCSM have been integrated into a new method called DUET [15].
INPS: predicting the impact of non-synonymous variations on protein stability from sequence
- http://bioinformatics.oxfordjournals.org/content/31/17/2816.long
- Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence.
- cite{fariselli_inps_2015}
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
- http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004556
- Predict the structural effect of multiple mutations.
- “Stability effects of all possible single-point mutations were estimated using the <BuildModel> module of FoldX”.
- We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased.
- cite{bednar_fireprot_2015}