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Subsections
Version History
Over the years there have been a number of different major DivCon versions that have
DivCon 4.5
The primary goal of this version is to capture the feedback we have received from our user base, and address the usability requirements for DivCon. Therefore, we have focused this version on removing as many barriers to entry as possible.
- A key example of the usability improvements available in this version is the integration of QMScore with DivCon. In previous versions, the user had to call a separate separate shell script that would in turn build the input files necessary to run QMScore and then call DivCon on each of these files to build the base data and use awk/grep to analyze the results. Version 4.5 now takes care of all QMScore functions internally and the user just needs to provide a target and a (set) of docked inhibitor(s) and use the -qmscore command line option. The final DivCon output file will then include the overall score of the target/inhibitor complex.
- Previous DivCon versions were almost completely reliant on a proprietary X,Y,Z formatted file to communicate a structure to DivCon. This dependency required the user to translate from his or her favorite format to the native DivCon format prior to actually using the software. This shortcoming is addressed by also accepting the mol2 format as an equal with the native format. In fact, in the case of a mol2 file that includes partial atomic charges, no further keywords or other options are required.
- Continuing the trend that was started with DivCon 4.0, the reliance on DelPhi for implicit solvation (self-consistent reaction field) calculations has been completely removed. DivCon 4.5 will automatically choose to run the SCRF calculation using its native DivPB code.
- As noted above, with version 4.5, DivCon has become much more automated where the only input required is a set of coordinates (mol2 or native DivCon) and a total charge. DivCon has all of the defaults and settings necessary to run a single point on most biomolecules.
- DivCon, just as with most molecular modeling software, is a keyword driven application. Now the user can also include command line options for many basic (and more advanced functions) including structure optimization, pairwise energy decomposition, and so on.
- The new version also includes a number of general stability and design improvements that may not be readily apparent to the user.
DivCon 4.0
- Through a complete optimization, audit, and significant redesign of the underlying source code, DivCon 4.x is now 2-4 times faster then DivCon03 depending upon the platform being used. These improvements are to the most fundamental aspects of the application, and they are not specific to any one Hamiltonian or optimization method. Therefore, you should begin to see the improvements right away.
- If you have a license to use the self-consistent reaction field (SCRF) algorithms, you now have a choice between using the previously utilized DelPhi module or our own, native Poisson-Boltzmann implementation. This latter approach is experimental in the research group, however it seems to be more stable for a wide variety of systems. To use the method, simply use the following keywords:
SCRF DIVPB SCALE=2.0
- In light of the new DivPB addition to DivCon, we have also added support for this new PB implementation in the QMScore script. To use the DivPB module instead of DelPhi in QMScore, you should add the following lines to your qmscore ?keywords? file (see the QMScore manual for more information):
DivPB=1
Grid=2.0
- You may have read a number of recent publications by the Merz Research Group detailing an approach to determine the NMR chemical shift of species within a biological system. DivCon 4.x is the first distributed version to include this code. To use this module, you will need to be sure that you have a license for our NMR module. Contact sales@quantumbioinc.com for more information.
- This version also includes a number of optimizations to increase the pairwise energy decomposition (PWD) performance. With recent submitted publications on the subject, this approach is gaining significant press.
- DivCon 4.x is also the first version to include a vastly improved license management module. No longer will DivCon simply ``self-destruct'' within an allotted amount of time. With this new version, the binary will specifically encode to your company, and you may upgrade at your own pace.
- The new version also includes a number of general stability and design improvements that may not be readily apparent to the user.
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