Software

As the software products of our research mature, we make them available at this website. Source code is available for some software, though based on feedback from our more applied collaborators, we are moving towards a web API model that will reduce installation and compilation headaches. Where software is open source, it is licensed under the Gnu General Public License v3.0. All software is distributed in the hope that it will be useful. If you use it to gather results in your research, please cite the associated papers below. Please refer all feature requests and bug reports to Brian Chen. 
 

VASP and VASP-E

VASP and VASP-E explore the idea that a solid geometric representation of molecular structures can be used to automatically deconstruct proteins into functional elements for the study of binding specificity. The package linked below includes VASP and other code necessary for the electrostatic analysis of protein-ligand binding cavities and protein-protein interfaces. Download here.

Associated publications:

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials. Brian Y. Chen, PLoS Computational Biology, 10(8): e1003792. doi:10.1371/journal.pcbi.1003792

VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity. Brian Y. Chen and Barry Honig. PLOS Computational Biology. 6(8): e1000881. doi:10.1371/journal.pcbi.1000881, 2010. 

 

SURFview

SURFview is a simple OpenGL renderer used to visualize .SURF files generated by VASP and other software from our lab. It also renders .pdb files for visual context. SURFview was used to generate figures in several recent papers. The binary release is compiled for the Windows platform.  Download here.

Associated publications:

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials. Brian Y. Chen, PLoS Computational Biology, in press.