Carter E S, Tung C S
Theoretical Division, Los Alamos National Laboratory, NM 87545, USA.
Comput Appl Biosci. 1996 Feb;12(1):25-30. doi: 10.1093/bioinformatics/12.1.25.
Using a new set of reduced coordinates developed for describing regular and unusual nucleic acid structures, we have revised our nucleic acid modeling tool NAMOT2. NAMOT2 is general in terms of modeling different nucleic acid structures. A set of modifiable libraries allows users to customize their modeling environment. With this set of libraries, NAMOT2 can be used to model non-canonical structures such as parallel-stranded, triple-stranded and quadruple-stranded nucleic acid molecules. For modeling irregular structures (junctions, hairpin loops, etc.), we introduce a structural recipe approach. The complete procedure using NAMOT2 to construct the structure of a specific molecule is treated as the recipe for that structural motif. The existing recipes can be modified to generate new recipes for different structural motifs. Several examples of nucleic acids with non-canonical structures were modeled using NAMOT2. These examples include a DNA-drug complex, a DNA cube, a six-arm junction and a curved DNA molecule.
通过使用一组为描述规则和异常核酸结构而开发的新简化坐标，我们对核酸建模工具NAMOT2进行了修订。NAMOT2在对不同核酸结构进行建模方面具有通用性。一组可修改的库允许用户自定义其建模环境。借助这组库，NAMOT2可用于对非经典结构进行建模，如平行链、三链和四链核酸分子。对于建模不规则结构（接头、发夹环等），我们引入了一种结构配方方法。使用NAMOT2构建特定分子结构的完整过程被视为该结构基序的配方。现有的配方可以修改，以生成针对不同结构基序的新配方。使用NAMOT2对几个具有非经典结构的核酸实例进行了建模。这些实例包括一个DNA-药物复合物、一个DNA立方体、一个六臂接头和一个弯曲的DNA分子。
