Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies.
Large amounts of data are being generated annually on the connection between the sequence, structure and function of proteins using site-directed mutagenesis, protein design and directed evolution techniques. These data provide the fundamental building blocks for our understanding of protein function, molecular biology and living organisms in general. However, much experimental data are never deposited in databases and is thus 'lost' in journal publications or in PhD theses. At the same time theoretical scientists are in need of large amounts of experimental data for benchmarking and calibrating novel predictive algorithms, and theoretical progress is therefore often hampered by the lack of suitable data to validate or disprove a theoretical assumption. We present PEAT (Protein Engineering Analysis Tool), an application that integrates data deposition, storage and analysis for researchers carrying out protein engineering projects or biophysical characterization of proteins. PEAT contains modules for DNA sequence manipulation, primer design, fitting of biophysical characterization data (enzyme kinetics, circular dichroism spectroscopy, NMR titration data, etc.), and facilitates sharing of experimental data and analyses for a typical university-based research group. PEAT is freely available to academic researchers at http://enzyme.ucd.ie/PEAT.
Farrell
Damien
D
Centre for Synthesis and Chemical Biology, School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
O'Meara
Fergal
F
Johnston
Michael
M
Bradley
John
J
Søndergaard
Chresten R
CR
Georgi
Nikolaj
N
Webb
Helen
H
Tynan-Connolly
Barbara Mary
BM
Bjarnadottir
Una
U
Carstensen
Tommy
T
Nielsen
Jens Erik
JE
D055592:Biophysical Phenomena; D017931:DNA Primers; D030562:Databases, Protein; D007700:Kinetics; D016296:Mutagenesis; D019906:Nuclear Magnetic Resonance, Biomolecular; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D015202:Protein Engineering; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers; D011506:Proteins