BioGem Blog

OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images, as they appear in journal articles, patent documents, textbooks, trade magazines etc., to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. The CACTUS OSRA tool parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure. Note that any software designed for optical recognition is unlikely to b...

VEGA ZZ is a free (for non-profit academic uses) molecular modelling suite. It consists of many third-party packages, which act as an interface to the VEGA ZZ software. OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. VEGA ZZ consists of an OSRA plug-in that acts as an interface to it. Moreover, it supports imaging devices such as cameras and image scanners for acquiring documents through the TWAIN interface. The VEG...

AutoDock is a free molecular modeling simulation suite mainly used for molecular docking. It consists of two programs, namely AutoGrid and AutoDock. The three variants of AutoDock are AutoDock 4.2.6 , AutoDock Vina 1.2.3 (a successor of AutoDock), and AutoDock GPU . AutoDock or Vina use PDBQT (Protein Data Bank (PDB), Partial Charge (Q), and Atom Type (T)) molecular structure file format for input and output. But, most molecular analysis and visualization tools accept the PDB file format. The video tutorial for converting AutoDock or Vina results in a complex PDBQT file format to PDB file format is below.

Protein Data Bank (PDB) file format is a representation of a three-dimensional (3D) structure of the protein and ligand data extracted by interpreting the experimental result of high-energy electromagnetic radiation (X-ray) or Nuclear Magnetic Resonance (NMR) through the computational method. The standard PDB file format was created by RCSB during the 1970s for parsing through software. The atomic coordinate entries of protein are represented by ATOM & TER fields, and ligand by HETATM field (given in the table below). Record Type Columns Description ATOM 1 - 4 "ATOM" 7 - 11 Atom serial number 13 - 16 Atom name 17 Alternate location indicator 18 - 20 Residue name 22 Chain identifier 23 - 26 Residue sequence number 27 Code for insertions of residues 31 - 38 X orthogonal Å coordinate 39 - 46 Y orthogonal Å coordinate 47 - 54 Z orthogonal Å coordinate 55 - 60 Occupancy 61 - 66 Temperature factor 73 - 76 Segment identifier 77 - 78 Element symbo...