NDLI: A dimensionality reduction approach to modeling protein flexibility

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A dimensionality reduction approach to modeling protein flexibility

Content Provider	ACM Digital Library
Author	Teodoro, Miguel L. Kavraki, Lydia E. Phillips, George N.
Abstract	Proteins are involved either directly or indirectly in all biological processes in living organisms. It is now widely accepted that conformational changes of proteins can critically affect their ability to bind other molecules and that any progress in modeling protein motion and flexibility will contribute to the understanding of key biological functions. However, modeling protein flexibility has proven a very difficult task. Experimental laboratory methods such as X-ray crystallography produce rather few structures, while computational methods such as Molecular Dynamics are too slow for routine use with large systems. A medium sized protein typically has a few thousands of degrees of freedom. This paper shows how to obtain a reduced basis representation of protein flexibility. We use the Principal Component Analysis method, a dimensionality reduction technique, to transform the original high dimensional representation of protein motion into a lower dimensional representation that captures the dominant modes of motions of the protein. Although there is inevitably some loss in accuracy, we show that we can obtain conformations that have been observed in laboratory experiments, starting from different initial conformations and working in a drastically reduced search space.
Starting Page	299
Ending Page	308
Page Count	10
File Format	PDF
ISBN	1581134983
DOI	10.1145/565196.565235
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2002-04-18
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

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