BioPhysConnectoR: Connecting sequence information and biophysical models.
BACKGROUND
One of the most challenging aspects of biomolecular systems is the understanding of the coevolution in and among the molecule(s).A complete, theoretical picture of the selective advantage, and thus a functional annotation, of (co-)mutations is still lacking. Using sequence-based and information theoretical inspired methods we can identify coevolving residues in proteins without understanding the underlying biophysical properties giving rise to such coevolutionary dynamics. Detailed (atomistic) simulations are prohibitively expensive. At the same time reduced molecular models are an efficient way to determine the reduced dynamics around the native state. The combination of sequence based approaches with such reduced models is therefore a promising approach to annotate evolutionary sequence changes.


RESULTS
With the R package BioPhysConnectoR we provide a framework to connect the information theoretical domain of biomolecular sequences to biophysical properties of the encoded molecules - derived from reduced molecular models. To this end we have integrated several fragmented ideas into one single package ready to be used in connection with additional statistical routines in R. Additionally, the package leverages the power of modern multi-core architectures to reduce turn-around times in evolutionary and biomolecular design studies. Our package is a first step to achieve the above mentioned annotation of coevolution by reduced dynamics around the native state of proteins.


CONCLUSIONS
BioPhysConnectoR is implemented as an R package and distributed under GPL 2 license. It allows for efficient and perfectly parallelized functional annotation of coevolution found at the sequence level.
Hoffgaard
Franziska
F
Theoretical Biology and Bioinformatics, Institute of Microbiology and Genetics, Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64289 Darmstadt, Germany. hoffgaard@bio.tu-darmstadt.de
Weil
Philipp
P
Hamacher
Kay
K
D001665:Binding Sites; D001703:Biophysics; D030541:Databases, Genetic; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D013329:Structure-Activity Relationship
D011506:Proteins