Simple procedure for conformation-family search in multidimensional torsion-angle space

Abstract

A method for studying conformation spaces in n dimensions has been developed. The method is used to calculate preferences of conformation families for the purpose of model building.

Geometric properties of nucleic acids with potential for autobuilding

“…The methods described above to locate phosphates and bases in electron-density maps are effective even at medium resolution. rotamers) for backbone building (Keating & Pyle, 2010;Pavelcik & Vanco, 2006;Pavelcik & Schneider, 2008;Schneider et al, 2004). Since the sugar ring tends to be rather flexible and less well described in the density, we replace C4 0 with C1 0 in the above definitions of and , and use the angles 0 ¼ ðC1 0 iÀ1 ÀP i ÀC1 0 i ÀP iþ1 Þ and 0 ¼ ðP i ÀC1 0 i ÀP iþ1 ÀC1 0 iþ1 Þ to facilitate the construction of the correct backbone from the list of putative phosphates and bases (Gruene, 2008;Keating & Pyle, 2010).…”

“…Several groups have investigated the use of preferred conformations of RNA (i.e. rotamers) for backbone building (Keating & Pyle, 2010;Pavelcik & Vanco, 2006;Pavelcik & Schneider, 2008;Schneider et al, 2004). While at lower resolution this is probably the only possible approach, this work focuses on a slightly different approach with more localized and possibly less bias-prone properties.…”

Structure Motivator: A tool for exploring small three-dimensional elements in proteins

“…However superimposition is not a practicable means of comparison for large sets of small structural motifs (hundreds and more). The most common practice is to display two-dimensional plots of the φ and ψ dihedral angles (Ramachandran plots [7]) at each residue [8-16]. Our program, Structure Motivator, also employs plots of dihedral angles of small three-dimensional structural elements.…”

Conformation families of protein fragments in multidimensional torsion-angle space

“…Protein conformations are mainly classified on the basis of hydrogen-bonding patterns and the two-dimensional Ramachandran plot (Ramachandran & Sasisekharan, 1963). Limited information is available for higher dimensional spaces (Pavelcik & Vanco, 2006;Sims et al, 2005).…”

“…A detailed analysis of twodimensional space has recently been published (Hovmö ller et al, 2002). Results for tripeptides in four-dimensional torsionangle space can be found in Pavelcik & Vanco (2006). Sims et al (2005) have analyzed higher dimensional (', ) n maps.…”