Pairwise contact potentials have a long, successful history in protein structure prediction. They provide an easily-estimated representation of many attributes of protein structures, such as the hydrophobic effect. In order to improve on existing potentials, one should develop a clear understanding of precisely what information they convey. Here, using mutual information, we quantified the information in amino acid potentials, and the importance of hydropathy, charge, disulfide bonding, and burial. Sampling error in mutual information was controlled for by estimating how much information cannot be attributed to sampling bias. We found the information in amino acid contacts to be modest: 0.04 bits per contact. Of that, only 0.01 bits of information could not be attributed to hydropathy, charge, disulfide bonding, or burial.
This chapter discusses analytic and algorithmic results for computational protein structure prediction by protein sequence-structure alignment, an approach also known as protein threading. Biological results are beyond the scope of this chapter, but may be found in 1, 2 , 3 , 4 . See also the chapter by D a vid Jones in this volume, which discusses another approach to protein threading.The chapter visits in turn: motivation, intuition, formalization, analysis, complexity, algorithm, computational cost, discussion, and conclusions. The early sections are tutorial in nature; the rest represent original research results. The overall conclusions are that: 1 computational techniques can render vast search spaces approachable by exploiting natural constraints; and 2 advances in knowledge-based objective functions and protein structural environment de nitions represent an important opportunity for future progress.A long-range goal of this work is to integrate structural and functional pattern recognition. The reader will notice that gapped block alignment is conceptually similar to block patterns, consensus patterns, weight matrices, pro le patterns, and hierarchical patterns, among many other gapped block pattern methods reviewed in 5 . Combined structural and functional pattern recognition is likely to prove more powerful than either one alone.
A short review of the threading approach to protein structure prediction, including presentation of some open statistical problems. Also discussed is one of the likely sources of the current limited success, that being the form of the pairwise potentials used in most threading approaches.
Unconsolidated sands form an extensive mantle across large parts of East Texas uplands. The exact geomorphic processes responsible for their formation are not known, but, on hill summit settings, these deposits are interpreted as either eolian sediments or as sand liberated by the in situ weathering of the underlying Tertiary age fluvial-deltaic sandstone bedrock. In order to identify which of these is the most likely formation process, we used detailed sedimentary analysis coupled with optically stimulated luminescence (OSL) dating of the sediment on seven samples from a single profile in Lee County, Texas. All OSL samples demonstrated that samples had been exposed to significant sunlight before they were deposited in the middle to late Holocene, thereby ruling out an in situ weathering origin. These results indicate that eolian sedimentation occurred during the middle to late Holocene and that archaeological sites within these deposits may be in good context and worthy of excavation.
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