SDF (Structure Data File) is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. “SDF” stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple compounds are delimited by lines consisting of four dollar signs ($$$$).

bend:sdf_example

• http://link.fyicenter.com/out.php?ID=571
• https://cactus.nci.nih.gov/SDF_toolkit/
• https://en.wikipedia.org/wiki/Chemical_table_file#SDF
• http://biotech.fyicenter.com/resource/sdf_format.html

PDB (Protein Data Bank)

Usar OpenBabel para convertir sdf to pdb (entre otros)

instalar OpenBabel en Debian Linux

sudo aptitude install openbabel openbabel-gui

ver formatos soportados

obabel -L formats %ver formatos soportados

comando de conversión de un sdf con múltiples moléculas a varios archivos pdb con los nombres de las moléculas

obabel ambinter_natural_compounds_3D.sdf -O dummy.pdb –split

http://vina.scripps.edu/tutorial.html

(http://vina.scripps.edu/manual.html#linux)

Descargar autodock de:

http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz

tar xzvf autodock_vina_1_1_2_linux_x86.tgz

./autodock_vina_1_1_2_linux_x86/bin/vina –help

./autodock_vina_1_1_2_linux_x86/bin/vina –receptor adt_ProteasaCOVID19_6lu7.pdbqt –ligand adt_Amb264320_model89.pdbqt –log test.log –center_x 1.52258 –center_y -15.1582 –center_z 11.2624 –size_x 12.9668 –size_y 18.0857 –size_z 18.2192

Covid-19 se llama a la enfermedad: “Coronavirus disease”. El virus se llama SARS-2-CoV