Methods Animals and Surgery Male 8-week-old C57Bl/6 mice were obtained from Crea Japan

s were calculated for each residue in antigen-antibody complexes and the single molecule structure with probe radius set as 1.4. Surface residues were those more than 12 SASA while those PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19762596 loss in binding of more than 12 were classified as get SAR 405 epitope on the antigen side and as paratope on the antibody side. Interaction energy simulation To create Proteochemometric models with different descriptors, binding affinity values of each antigen-antibody complex were simulated by Hex. To guarantee the antigen-antibody complexwa maintain the combination position, Receptor Rotation Range, Ligand Rotation Range, Twist Range were set as 0 and Distance Range was set as 1; Correlation type was set as shape & electrostatics. The interaction energies of 429 antigen-antibody complexes were calculated and listed in S2 and S3 Interaction interface coordinate system generation To build the protein fingerprint and EPIF, interaction coordinate system was firstly established. Here, residue ri of the antigen-antibody complex was simplified as a point Pi by averaging its atoms’ coordinates. Then, the geometric center of epitope and paratope were calculated by averaging the coordinate of epitope residue and paratope residue respectively. Later, the geometric center of interaction interface was calculated by averaging the coordinate of all the residues from both epitope side and paratope side. Based on those three points, our coordinate system can be generated. Protein fingerprint generation There exist server protein description methods which contains structure information mainly focusing on coordinate information, distance information and bond type/angel information of protein structures. However, previous studies illustrated that the interface features of epitope-paratope interaction may relate more to the amino acid composition, local structural and physical-chemical environment on the interaction surface. It is widely reported that physical-chemical features such as hydrophobic interaction, hydrogen-bond interaction and electrostatic interaction play essential roles in the antigen-antibody interaction 7 / 15 PCM Modeling by New Protein Fingerprints and EPIF Fig 2. Illustration of antigen-antibody interaction coordinate PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19761586 system. Yellow and green balls represent the simplified point Pi of each residue ri in the coordinate system; point Cp represents the geometric center of the paratope side while point Ce represents the geometric center of the epitope side; point C represents the geometric center of the interaction interface. doi:10.1371/journal.pone.0122416.g002 interface. Here, fingerprints containing both structural features and physical-chemical environment features were established to describe the structure features of antibody in the interaction interface. Structure fingerprint generation through cylinder model. By setting a plane through ! point C and perpendicular to Vector Ce Cp, a virtual interaction interface was generated. This “virtual interaction interface” was set as the X-Y axis plane. With point C set as the origin, the Z axis was settled by the normal vector ! of X-Y plane towards to the paratope side. Then the n rotating plane was established by the X-Y-Z axis to generate the structure fingerprints. Along with a size-defined rotating plane revolving around axis Z, each of the surface residues can be punched into the certain position of the cylinder model. In order to contain enough residues in interaction interface, different plane size and grid r