of Nucleic Acid Containing Structures
About this Atlas
The NDB Atlas of Nucleic Acid Structures was developed to highlight
aspects of each structure in the NDB.
How were the Atlas pages generated?
Each page is generated directly from NDB using an XML translator
which formats the data contained in each NDB file. Pictures present
on the Atlas pages were generated by different software. Blocview (a
program developed by Xiang-Jun Lu) was used to generate pictures
of the asymmetric units and biological units for x-ray structures
and was used to generate the representative model pictures for NMR
structures. RNAview (a graphics program developed by Huanwang Yang
in collaboration with Fabrice Jossinet and Eric Westhof) was used
to generate two-dimensional represenations of RNA structures. MaxIT
(Macromolecular Exchange Input Tool developed by Zukang Feng and
John Westbrook) was used to generate crystal packing pictures for
x-ray structures and ensemble pictures for NMR structures.
The Atlas has evolved into its present form due to the participation
of several groups of students. The original version of the Atlas
was created by the following students: Lindsey Lair, Kavin Mistry,
Ketan Patel, Audrey Swamy, Judy Tsai, and Julie Woda. The second
version of the Atlas was part of an NDB Summer Program, with Sam
Engel, Mike Mehnert, Ketan Patel, Ivan Sirett, and Maria Steffero
participating. Additional developments on the Atlas were then made
by Debra West and Sesh Venugopal. The current version of the Atlas
is a result of the NDB Summer 2002 program, with Goran Aleksic,
Joanna de la Cruz, Gregory Donahue, Dipannita Kalyani, Dan Kulp,
and Hari Narayan participating.
How are the images colored?
In the nucleotide block models, adenine is red, thymine is blue,
cytosine is yellow, guanine is green, and uracil is cyan.
In the atom stick models, carbon is black, oxygen is red, nitrogen
is blue, and phosphates are orange.
How are modifications in the sequence shown?
In the sequence section of an atlas page, modified bases are
designated with the modifier following the base. A modifier
designated after the p in the compound name indicates that the sugar phosphate
How is the Atlas organized?
The Atlas is first divided by how the structures were determined: by
X-ray crystallographic or NMR experiments. Gallery index pages,
which include images for each structure on the page, and plain text index
pages, are offered.
These index pages are then divided into several categories that were
created by using a variety of constraint parameters, such as conformation
type or presence of modifications, drugs, etc. Several structures appear
in multiple categories.
How are the Atlas pages used?
The Atlas pages serve many purposes. They are an invaluable aide
in checking the structures contained within the NDB. They serve
as a teaching tool for the many students who have created and checked
the Atlas pages. Test versions of the Atlas have been very effective
in teaching students at all levels about nucleic acid structure.
How can these Atlas pages be accessed?
These pages are accessible from the Atlas section of the NDB WWW
site and as an output option from the NDB WWW Interface.