Paper Info
Title
PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides.
Abstract
Pseudo-Rotational Online Service and Interactive Tool (PROSIT) designed to perform complete pseudorotational analysis of nucleosides and nucleotides is described. This service is freely available at http://cactus.nei.nih.gov/prosit/. Files containing nucleosides/nucleotides or DNA/RNA segments, isolated or bound to other molecules (e.g., a protein) can be uploaded to be processed by PROSIT. The service outputs the pseudorotational phase angle P, puckering amplitude v(max), and other related information for each nucleoside/nucleotide detected. The service was implemented using the chemoinformatics tooWt CACTVS. PROSIT was used for a survey of nucleosides contained in the Cambridge Structural Database and nucleotides in high-resolution crystal structures from the Nucleic Acid Database. Special cases discussed include nucleosides having constrained sugar moieties with extreme puckering amplitudes, and several specific DNA/RNA helices and protein-bound DNA oligonucleotides (Dickerson-Drew dodecamer, RNA/DNA hybrid viral plypurine tract, Z-DNA enantiomers, B-DNA containing (L)-alpha-threofuranosyl nucleotides, TATA-box binding protein/TATA-box complex, and DNA (cytosine C5)-methyltransferase complexed with an oligodeoxyribonucleotide containing transition state analogue 5,6-dihydro-5-azacytosine). When the puckering amplitude decreases to a small value, the sugar becomes increasingly planar, thus reducing the significance of the phase angle P. We introduce the term "central conformation" to describe this part of the pseudorotational hyperspace in contrast to the conventional north and south conformations.
Year
DOI
Venue
2004
10.1021/ci049881+
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
Keywords
DocType
Volume
transition state,crystal structure,nucleotides,high resolution,nucleic acid,dna hybridization
Journal
44
Issue
ISSN
Citations 
5
0095-2338
0
PageRank 
References 
Authors
0.34
3
5
Name
Order
Citations
PageRank
Guangyu Sun100.34
Johannes H. Voigt29312.24
Igor V. Filippov3747.42
Victor E. Marquez400.34
Marc C. Nicklaus518630.38