Cluster distance geometry of polypeptide chains

Distance geometry has been a broadly useful tool for dealing with conformational calculations. Customarily each atom is represented as a point, constraints on the distances between some atoms are obtained from experimental or theoretical sources, and then a random sampling of conformations can be calculated that are consistent with the constraints. Although these methods can be applied to small proteins having on the order of 1000 atoms, for some purposes it is advantageous to view the problem at lower resolution. Here distance geometry is generalized to deal with distances between sets of points. In the end, much of the same techniques produce a sampling of different configurations of these sets of points subject to distance constraints, but now the radii of gyration of the different sets play an important role. A simple example is given of how the packing constraints for polypeptide chains combine with loose distance constraints to give good calculated protein conformers at a very low resolution. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1305–1312, 2004Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34697/1/20056_ftp.pd

BALL - biochemical algorithms library 1.3

<p>Abstract</p> <p>Background</p> <p>The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.</p> <p>Results</p> <p>Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.</p> <p>Conclusions</p> <p>BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at <url>http://www.ball-project.org</url>. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.</p