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====== File Formats ======

===== SDF =====

Structure Data Format (SDF) is a chemical file formats to represent multiple chemical structure records and associated data fields. SDF was developed and published by Molecular Design Limited (MDL) and became the the most widely used standard for importing and exporting information on chemicals. Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). 

[[bend:sdf_example|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 =====

The Protein Data Bank Format (PDB) is commonly used for proteins but it can be used for other types of molecules as well. It was originally designed as, and continues to be, a fixed-column-width format and thus officially has a built-in maximum number of atoms, of residues, and of chains; this resulted in splitting very large structures such as ribosomes into multiple files. However, many tools can read files that exceed those limits.

//Some molecular modeling tools write nonstandard PDB-style files that adapt the basic format to their own needs.//

The Protein Data Bank (pdb) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format. 

[[bend:pdb_example|bend:pdb_example]]

  * http://link.fyicenter.com/out.php?ID=569
  * https://en.wikipedia.org/wiki/Chemical_file_format#Protein_Data_Bank_Format

===== PDBQT =====

PDBQT format is very similar to PDB format but it includes partial charges ('Q') and AutoDock 4 (AD4) atom types ('T'). There is one line for each atom in the ligand, plus special keywords indicating which atoms, if any, are to be flexible during the AutoDock experiment.

[[bend:pdbqt_example|bend:pdbqt_example]]

  * https://www.mdanalysis.org/docs/documentation_pages/coordinates/PDBQT.html
  * http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file

====== File Conversion ======

https://en.wikipedia.org/wiki/Chemical_file_format#Converting_Between_Formats

====== SDF to PDB ======

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**

{{:bend:amb264320.png?nolink&400|}}

====== PDB to PDBQT using autodocktools (adt) ======

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


====== Docking mediante Autodock en Linux ======

(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

====== SARS-2-CoV ======

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