The Bio Chemical Library (BCL)

The Bio Chemical Library (BCL) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data.

The BCL contains the widely used secondary structure prediction program JUFO, a folding algorithm that assembles secondary structure elements, and loop construction tools that complete protein backbones. With this series of protocols the BCL allows construction of backbone models for large and membrane proteins from the primary sequence. Among its unique strengths are the incorporation of sparse and low resolution data into folding simulations.

Additionally, the BCL contains a suite of cheminformatics tools that allow construction of quantitative structure-activity-relation (QSAR) models for virtual screening, pharmacophore mapping, and drug design.

The BCL is comprised of over one thousand classes organized in 38 namespaces with approximately 200,000 lines of code that form a collection of C++ algorithms developed since 2005. The BCL and its applications have become popular, with more than 50,000 users of the online servers and more than 200 academic licensees.


A movie showing the evolution of the bcl source and include tree made with Gource

Evolution of bcl

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A code swarm video that illustrates individual developer contributions and the expanding diversity of bcl projects and applications. In an academic setting, it is easy for code to become abandoned as students graduate and leave the lab. The ongoing evolution of the bcl speaks to its extensibility and adherence to modular, object-oriented, design.

BCL Development

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Current Project Members: Jens Meiler , Jeff Mendenhall
Alumni Project Members: Mert Karakas , Ralf Mueller , Rene Staritzbichler , Nils Woetzel , Mariusz Butkiewicz , Steffen Lindert , Sten Heinze , Nathan Alexander , Edward W. Lowe Jr , Pedro Teixeira , Brian Weiner , Gregory Sliwoski , Sandeep Kothiwale , Dan Viox , Daniel Putnam