Computes direct and indirect readout energies and Z-scores. ReadOut can be used to obtain the energy Z-scores based on our force fields. It takes the coordinate data of a protein-DNA complex and calculates its conformational parameters and base-amino acid contacts. It can be used to analyze the interaction energy, the DNA conformation energy, and the relative contributions to the specificity from direct and indirect readouts. Moreover, it aims to check the quality of protein-DNA complex structures, and to engineer proteins and target DNAs.
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan; Computational Biology Group, Neutron Biology Research Center, Japan Atomic Energy Agency (JAEA), Kyoto, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan; Department of Biosciences, Jamia Millia Islamia University, New Delhi, India
ReadOut funding source(s)
Supported in part by Grants-in-Aid for Scientific Research 16014219, 17017030, 17054031 and 16014226 from Ministry of Education, Culture, Sports, Science and Technology in Japan.