pyDock performance in 5th CAPRI edition: from docking and scoring to binding affinity predictions and other challenges
Visualitza/Obre
Tipus de documentText en actes de congrés
Data publicació2015-05-05
EditorBarcelona Supercomputing Center
Condicions d'accésAccés obert
Llevat que s'hi indiqui el contrari, els
continguts d'aquesta obra estan subjectes a la llicència de Creative Commons
:
Reconeixement-NoComercial-SenseObraDerivada 3.0 Espanya
Abstract
Proteins form the executive machinery underlying all
the biological processes that occur within and between cells, from
DNA replication to protein degradation. Although genome-scale
technologies enable to clarify their large, intricate and highly
dynamics networks, they fail to elucidate the detailed molecular
mechanism that underlies the protein association process. Therefore,
one of the most challenging objectives in biological research is to
functionally characterize protein interactions by solving 3D complex
structures.
This is, however, not a trivial task as confirmed by the large gap
that exist between the number of complexes identified by large-scale
proteomics efforts and those for which high-resolution 3D
experimental structures are available. For these reasons,
computational docking methods, aimed to predict the binding mode
of two proteins starting from the coordinates of the individual
subunits, are bound to become a complementary approach to solve
the structural interactome.
Given its importance, the field of protein docking has
experienced an explosion in recent years partially propelled by
CAPRI (http://www.ebi.ac.uk/msd-srv/capri/). CAPRI (Critical
Assessment of PRedicted Interaction) is a community-wide blind
experiment aimed at objectively assessing the performance of
computational methods for modeling protein interactions by inviting
developers to test their algorithms on the same target system and
quantitatively evaluating the results.
In order to test pyDock,1 a docking scoring algorithm developed
in our group, the PID (Protein Interaction and Docking) group of the
BSC Life Science Department, we have participated in all the 15
targets (T46 to T58) of the 5th CAPRI edition (2010-2012). Our
automated protocol confirmed to be highly successful to provide
correct models in easy-to-medium difficulty protein-protein docking
cases placing among the Top5 ranked groups out of more than 60
participants.
Key words: Complex structure, CAPRI, protein-protein
docking, pyDock, protein interactions.
CitacióPallara, Chiara [et al.]. pyDock performance in 5th CAPRI edition: from docking and scoring to binding affinity predictions and other challenges. A: "BSC Doctoral Symposium (2nd: 2015: Barcelona)". 2nd ed. Barcelona: Barcelona Supercomputing Center, 2015, p. 99-100.
Fitxers | Descripció | Mida | Format | Visualitza |
---|---|---|---|---|
pyDock_DS2105-BoAv11-27.pdf | 210,7Kb | Visualitza/Obre |