Abstract
Global minimal structure of protein/enzyme is energetically compromised that maintains an intricate balance between the rigidity and the flexibility. Such a state makes it interactive to its ligand molecules. Although protein data bank files (PDB) may have achieved the state, in many situations minimization has been crucial to overcome unwanted steric clashes, and other conformational strains. It is more so, when orthologous PDB structures that are intended in a given study, show variations in resolution, R-factor, shell-water contents, loop characteristics etc. Here, a fully automated procedure of minimization would be highly useful. AUTOMINv1.0 is such an automation of minimization that runs on any number of structure files with any number of chains in them along with the inclusion of selective/non-selective shell-waters interacting with polar and or non-polar atom-types of protein. Comparison of the mean binaryitems of salt-bridges of minimized and un-minimized structures (chains > 100) of nucleoside diphosphate kinase from mimi virus shows dramatic improvements in the earlier. Again, the mean steric clashes of 2AZ3.pdb are reduced upon minimization. Remarkably, the observed steric clashes between shell-waters and atom-types of protein are seen to be removed upon minimization. Taken together, AUTOMINv1.0 is an automation of minimization that finds applications in structural bioinformatics.
Highlights
With the advent of protein's structure database, the concept of local-dataset-based proteomic scaled bioinformatics analyses is making rapid progress
Since candidate structures against a given UniProt ID and orthologous structures are many in the database, and since each of these structures has different state properties and experimental details, minimization in these cases seems to be crucial [1]
The procedure is far more complicated, when i] a protein data bank (PDB) file possesses homomeric/heteromeric chains in them, ii] a family of PDB structures intended for a proteomicscaled-bioinformatics-studies and, iii] inclusion of crystallographic shell-waters are required
Summary
With the advent of protein's structure database, the concept of local-dataset-based proteomic scaled bioinformatics analyses is making rapid progress. The procedure is far more complicated, when i] a PDB file possesses homomeric/heteromeric chains in them, ii] a family of PDB structures intended for a proteomicscaled-bioinformatics-studies and, iii] inclusion of crystallographic shell-waters are required. For a given structure with many chains, the details on expression system, crystallization conditions, R-factors, and ground-state potential energy are identical, candidate PDBs of a given family have variations in these details, which could largely be improved upon minimization. Such mass-scaled minimization could suitably be achieved by the use of a fully automated procedure. It is compiled using AWKA (URL: http://awka.sourceforge.net/index.html) Presently we are actively engaged in developing a web interface to integrate AUTOMINv1.0 and other structure related programs of our laboratory such as ADSBET [14] and COSURIM [15] such that their availability could reach to academic users within a unique web service
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