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ProteinVolume: calculating molecular van der Waals and void volumes in proteins

Calvin R Chen, George I Makhatadze
2015 BMC Bioinformatics  
ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular  ...  The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution  ...  The sum of all van der Waals volume probes is calculated and reported as van der Waals protein volume (V VDW ).  ... 
doi:10.1186/s12859-015-0531-2 pmid:25885484 pmcid:PMC4379742 fatcat:oh2yc5l2e5bcnbv7gs7ww3uxuu

Molecular determinant of the effects of hydrostatic pressure on protein folding stability

Calvin R. Chen, George I. Makhatadze
2017 Nature Communications  
The molecular details of this difference in sign of volume changes have been puzzling the field for the past 50 years.  ...  These observations suggest that volume changes upon protein unfolding can be both positive and negative.  ...  The sum of all van der Waals volume probes is calculated and reported as van der Waals protein volume (V vdW ).  ... 
doi:10.1038/ncomms14561 pmid:28169271 pmcid:PMC5309723 fatcat:7ooga36br5fi3j3belbp4fvt5a

The relationships between genetic diseases and the structures of protein and their interactions

Sirawit Ittisoponpisan, Michael Sternberg, Thailand
2020
This study shows that pleiotropic proteins have unique properties: 1) they are enriched in disease-associated SAVs and rare neutral SAVs, 2) they tend to contain disordered regions, 3) they tend to have  ...  a higher number of protein-protein interactions, and 4), they are more specific to diseases of certain classes such as neoplasm, nervous system, and congenital malformation.  ...  ProteinVolume calculates the molecular surface of a protein and uses flood-fill algorithm to calculate intramolecular void volumes.  ... 
doi:10.25560/78637 fatcat:xcq5n5jbe5gpnm77vq37ffl2bq

ELUCIDATING THE HMG-COA REDUCTASE REACTION MECHANISM USING PH-TRIGGERED TIME-RESOLVED X-RAY CRYSTALLOGRAPHY

Vatsal Purohit
2021
occurs through the generation of two intermediates, mevaldehyde and mevaldyl-CoA (Shown in Fig 1.1).  ...  To investigate the factors limiting enzymatic activity in the crystal, we investigated the effects of pH and specific ions in the crystallization environment.  ...  Chen, C.R. and G.I. Makhatadze, ProteinVolume: calculating molecular van der Waals and void volumes in proteins. BMC bioinformatics, 2015. 16(1): p. 101-101. 109.  ... 
doi:10.25394/pgs.17161532 fatcat:axwvc4f26jbi5cpfq3tdffpzqu