Author: Santiago Restrepo-Castillo
Hi folks! These are the codes I wrote during my undergraduate studies in Biomedical Engineering at Universidad EIA (Medellín, Colombia). I am currently a graduate student at the Mayo Clinic Graduate School of Biomedical Sciences (Rochester, MN, USA), pursuing a Ph.D. in Virology and Gene Therapy. I can be reached at my professional email address: restrepocastillo.santiago@mayo.edu. Find short descriptions of the codes below.
Elastic Network Model-based Normal Mode Analysis: This is the most important code. This algorithm allows you to find the natural frequencies and normal modes of vibration of a biomolecule with a known crystal structure. All you need is the PDB file of the molecule and to assign certain parameters (explained in the code).
Normal modes animator: This algorithm allows to animate any available normal modes of vibration of a biomolecule previously analyzed via normal mode analysis.
Experimental B-factors: This algorithm allows to retrieve the experimental B-factors of a biomolecule from its PDB file.
Theoretical B-factors: This algorithm allows to calculate the B-factors of a biomolecule as a function of its natural frequencies and normal modes of vibration. Logically, normal mode analysis of the biomolecule must have been previously conducted.
Molecule grapher: This versatile algorithm allows to obtain graphs or animations of a biomolecule. Some of the features of this program include: possibility of highlighting the assymetric unit of the crystal structure, drawing the springs between atomic pairs, color mapping the biomolecule according to its flexibility profile, obtaining an all-atom graph of the biomolecule highlighting its alpha carbons backbone, create a rotating animation of the biomolecule, etc.
Color bar creator: This simple piece of code allows to create color bars for visual purposes.