We selected few compound-PDB interactions for COAD: FABP6 - Abemaciclib, GLTP - Nilotinib, PTPRN - Venetoclax, and VEGFA - Venetoclax. Note: a drug name corresponds to more compounds in PubChem, and a gene name corresponds to more PDB structures. For these figures, we selected a PDB for each gene and a compound for each drug name.

Gene = FABP6 | PDB = 2mm3 | Drug name = abemaciclib | PubChemID = 4622050

Docking-PDBQT Target-PDBQT

Vina binding modes (rotate, zoom, full screen, selection, etc.):

Visual details about drug - protein interactions:

Interactions:

Vina output (binding modes, seed for reproductibility):

Vina configuration file (searching box position and dimension, exhaustiveness):

Gene = GLTP | PDB = 3s0i | Drug name = nilotinib | PubChemID = 644241

Docking-PDBQT Target-PDBQT
Vina binding modes (rotate, zoom, full screen, selection, etc.):

Visual details about drug - protein interactions:

Interactions:

Vina output (binding modes, seed for reproductibility):

Vina configuration file (searching box position and dimension, exhaustiveness):

Gene = PTPRN | PDB = 3np5 | Drug name = venetoclax | PubChemID = 49846579

Docking-PDBQT Target-PDBQT
Vina binding modes (rotate, zoom, full screen, selection, etc.):

Visual details about drug - protein interactions:

Interactions:

Vina output (binding modes, seed for reproductibility):

Vina configuration file (searching box position and dimension, exhaustiveness):

Gene = VEGFA | PDB = 4gls | Drug name = venetoclax | PubChemID = 49846579

Docking-PDBQT Target-PDBQT
Vina binding modes (rotate, zoom, full screen, selection, etc.):

Visual details about drug - protein interactions:

Interactions:

Vina output (binding modes, seed for reproductibility):

Vina configuration file (searching box position and dimension, exhaustiveness):


Acknowledgements: This work was supported by "Collaborative Project in Genomic Data Integration (CICLOGEN)" PI17/01826 funded by the Carlos III Health Institute from the Spanish National plan for Scientific and Technical Research and Innovation 2013–2016 and the European Regional Development Funds (FEDER), the “Galician Network for Colorectal Cancer Research” (Ref. ED431D 2017/23), and finally by the Spanish Ministry of Economy and Competitiveness through the project BIA2017-86738-R and through the funding of the unique installation BIOCAI (UNLC08-1E-002, UNLC13-13-3503) and the European Regional Development Funds (FEDER) by the European Union. Additional support was offered by the Accreditation, Structuring, and Improvement of Consolidated Research Units and Singular Centers (ED431G/01), funded by the Ministry of Education, University and Vocational Training of Xunta de Galicia endowed with EU FEDER funds.