molecular operating environment software moe 2018 version  (Chemical Computing Group)

Journal: Viruses

Article Title: Structural Insights into the Interaction of Filovirus Glycoproteins with the Endosomal Receptor Niemann-Pick C1: A Computational Study

doi: 10.3390/v13050913

Figure Lengend Snippet: Interface contact residues in the GPcl–NPC1complexes. ( A ) Residue contact pairs of the GPcl–NPC1 interfaces for EBOV, SUDV, and RAVV were analyzed using the MOE software (version 2018; Chemical Computing Group, Montreal, Canada). Residue–residue contact pairs that appeared in at least 50% of the 1500 MD simulation frames are shown for EBOV (blue), SUDV (red), and RAVV (yellow) GPcl–NPC1 complexes. In each panel, the light, intermediate dark, and darkest colors represent the contact pairs containing van der Waals interactions (vdW), vdW + hydrogen bonds (hb), and vdW + hb + salt bridges (sb), respectively. Amino acid residues that are distinct from those of EBOV GPcl are shown in red. The numbering scheme for GPcl was adapted from EBOV. ( B ) Venn diagram for the number of residue contact pairs observed for EBOV (blue), SUDV (red), and RAVV (yellow) GPcl–NPC1 complexes.

Article Snippet: Residue–residue contacts between NPC1-C and GPcl from EBOV, SUDV, and RAVV were analyzed using the Protein Contacts in Molecular Operating Environment (MOE) software (version 2018; Chemical Computing Group, Montreal, QC, Canada).

Techniques: Software

Journal: Viruses

Article Title: Structural Insights into the Interaction of Filovirus Glycoproteins with the Endosomal Receptor Niemann-Pick C1: A Computational Study

doi: 10.3390/v13050913

Figure Lengend Snippet: Differences in the GPcl–NPC1 binding structures between EBOV, SUDV, and RAVV. ( A ) Residue contact pairs of the GPcl–NPC1 interfaces for EBOV, SUDV, and RAVV were analyzed using the MOE software (version 2018; Chemical Computing Group, Montreal, Canada). Residue–residue contact pairs that appeared in at least 50% of the 1500 MD simulation frames, are shown for EBOV (blue), SUDV (red), and RAVV (yellow) GPcl–NPC1 complexes. In each panel, the light, intermediate dark, and darkest colors represent the contact pairs containing van der Waals interactions (vdW), vdW + hydrogen bonds (hb), and vdW + hb + salt bridges (sb), respectively. Amino acid residues that are distinct from those of EBOV GPcl are shown in red. The numbering scheme for GPcl was adapted from EBOV. ( B ) Venn diagram for the number of residue contact pairs observed for EBOV (blue), SUDV (red), and RAVV (yellow) GPcl–NPC1 complexes.

Article Snippet: Residue–residue contacts between NPC1-C and GPcl from EBOV, SUDV, and RAVV were analyzed using the Protein Contacts in Molecular Operating Environment (MOE) software (version 2018; Chemical Computing Group, Montreal, QC, Canada).

Techniques: Binding Assay, Software