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Fig. 5 | BMC Bioinformatics

Fig. 5

From: Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab

Fig. 5

No non-bonded interactions between the BC-loop and PD-L1. a The non-bonded interaction energies between PD-1 and PD-L1 (red) and PD-1 and nivolumab (blue) are shown as a histogram and are grouped in packages of 100 kJ mol− 1. The non-bonded interaction energy between PD-1 and PD-L1 ranges from − 1000 to − 2000 kJ mol− 1 with a peak of 2700 frames at − 1600 kJ mol− 1. The energy distribution between PD-1 and nivolumab ranges from − 500 to − 1200 kJ mol− 1. The peak is at − 900 kJ mol− 1 with 3100 occurrences. b The non-interaction energies between the BC-loop and two ligands is grouped into packages of 10 kJ mol− 1. The energy between the BC-loop and PD-L1 peaks at-10 kJ mol− 1. This peak occurs due to the minor distortions (between 0 and − 1 kJ mol− 1). The non-bonded interaction energy between the BC-loop and nivolumab ranges from 0 to − 250 kJ mol− 1

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BMC Bioinformatics

ISSN: 1471-2105

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