BioAssemblyModeler (BAM) Homology Modeling of Protein Homo- and Heterooligomers
Current Version: 220.127.116.11, Release Version
Feb 10, 2017. Important: major BAM update is released, version 2.1
This update includes our significant efforts to keep BAM up to date and useful since we first published the BAM paper in 2014 and subsequently updated its databases and workflow.
Recently we updated all underlying databases up to the beginning of 2017. It allows to build your target models based on new templates. The database updates include Relational PDB database, PDBAA sequence database, sequence alignment profiles, etc.
Technical: If you wish to use new templates up to 2017 for your target sequences, you need to update BAM to 2.1. Older versions of BAM (lower than 2.1: 2.0.*.*) are NOT compatible with our updated databases. The database format changed and requires BAM application update. Older BAM application versions are still supported but with no database update. You can easily update BAM automatically through the application itself: BAM -> Tools -> Update. Once BAM is updated, it will suggest to update its databases: BAM -> Tools -> Update Databases.
BAM stands for BioAssemblyModeler. BAM is a graphical user interface (GUI) application for building protein homooligomers and heterooligomers by means of comparative (homology) modeling.
As input BAM accepts one to six different amino acid "Target" sequences. A list of available template protein complexes grouped by their domain architecture is provided during the modeling process. The architecture list is automatically sorted with the most similar domain content of the Target presented first. The template list indicates whether a proposed template complex contains any additional protein subunits not present in the target that may be of biological interest. Within 10-60 mins, the user can expect to build a homology model of a biologically active protein complex consisting of all or some input protein sequences. Please note that modeling of insertion and deletion regions (indels) is not included in the current version of BAM. The user will need to model indels with third-party software.
Windows users: BAM is compatilble with Microsoft Windows, all editions with .NET support: XP, Vista, 7, 8, 10 and either 32bit or 64bit.
Linux and Mac users: Windows can be installed on Linux and all recent Macintosh machines using free virtualization software such as VirtualBox, http://virtualbox.org). We have tested BAM using VirtualBox on both Linux and Mac OS and it functions well. Please pay attention that you still need to have a Windows license (DVD, CD, image, etc).
The open-access BAM publication can be found here.
Please cite us:
Shapovalov MV, Wang Q, Xu Q, Andrake M, Dunbrack RL Jr (2014) BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers. PLoS ONE 9(6): e98309. doi:10.1371/journal.pone.0098309
In Beginner Mode BAM enables a built-in navigation system guiding the user through all modeling steps. It informs the user what to do next in a status bar. In a continuous flow the navigation system highlights appropriate Main Menu items, textboxes, buttons and other user interface controls. The user should be able to use the software without extensive consultation of the software manual, which is provided for more detailed information.
Below are the steps of a complete homology modeling cycle. All these steps are done through the graphical interface and are prompted in Beginner Mode. Please click on the individual steps below or refer for additional help to Modeling Steps In Detail and Tutorial Videos.