The structure-filter page offers two options for the user to define a set of structures. First, one can make selections based on a combination of the following features: the experimental method used to determine the structure; the molecular contents; the conformational characteristics of the constituent base-pair steps; and the resolution cutoff. By specifying the experimental method, the user can examine structures obtained by X-ray, NMR, or both approaches. The choice of molecular contents refers to the other molecules present in the experimental structure: proteins; drugs or other small molecules; bound waters; metal ions. The conformational option allows the user to select structures, identified with the 3DNA software, with local conformational features characteristic of left-handed Z DNA structures or with a given number or fraction of base-pair steps with phosphorus atoms in arrangements typical of those found in right-handed A- and B-DNA double helices, in intermediate AB states, and in the TA geometry first identified in the complex of DNA with the TATA-box-binding protein [1]. The resolution cutoff affects only the collection of X-ray structures. The NMR structures in the database have an arbitrarily assigned resolution of zero, which will lie always within the cutoff limit.

The second option lets the user enter a list of PDB or NDB structural identifiers (IDs), which the server checks for accuracy. This option allows the user to perform searches elsewhere, such as the integrated search at the NDB or the advanced search at the PDB, and then import the findings into the 3DNALandscapes interface for conformational analysis.

After clicking 'next', a list of structures with brief descriptions is displayed in a table with sorting and paging capabilities.

The selected PDB structures are presented in a Grid-view table with sorting and paging capabilities. The PDB and NDB identifiers are directly linked to the web pages respectively associated with the specified structures in the PDB and NDB. The structural method used to determine the structure and a brief description of the structures are also displayed. In this table, more detailed classification is provided.

The user can also modify the list at this point in the search by specifying the relevant PDB ID(s) to be removed or added.

The grid-view table allows the user to sort the columns by clicking on the column header, to jump to a particular page, and to change the display size of a page.

The "Export data" link in the top-right corner allows the user to download the data file, which contains every entry in the Grid-view table. Users are encouraged to download the data and conduct further analyses offline.

Finally, the user has the option of selecting a representative structure (the first structure) or the complete ensemble of structures associated with an NMR-based file. It worth noting that that selection of ensembles can lead to time delays in the analysis and visualization of large quantities of data and also may bias the statistical results. The choice can be useful, however, if the user is interested in the conformational trends associated with the DNA included in a single NMR structure file.

The parameter panel allows the user to choose the conformational parameters of interest. The parameter list includes various quantities associated with the DNA backbones, sugar-base side groups, base pairs, base-pair steps, and complementary strands.

Each section is detailed below:

The backbone options allow the user to access two sets of conformational parameters within the set of selected structures: (i) Phosphodiester backbone torsions - the six phosphodiester-backbone torsion angles - &alpha (O3'-P-O5'-C5'), &beta (P-O5'-C5'-C4'), &gamma (O5'-C5'-C4'-C3'), &delta (C5'-C4'-C3'-O3'), &epsilon (C4'-C3'-O3'-P), &zeta (C3'-O3'-P-O5') - along the sugar-phosphate backbone; and (ii) Virtual parameters - the distances d_(P-P) between phosphorus atoms on successive nucleotides. The distances are expressed in Ångstrom units and the angles are assigned values over the range [-180,180] degrees.

The sugar-base side-group options include: (i) Side-group torsion - the glycosyl torsion &chi (O4'-C1'-N9-C4 or O4'-C1'-N1-C2) describing the orientation of a purine (R) or pyrimidine (Y) with respect to the sugar ring; (ii) Sugar-ring torsion angles - the five internal sugar ring torsion angles - &nu₀ (C4'-O4'-C1'-C2'), &nu₁ (O4'-C1'-C2'-C3'), &nu₂ (C1'-C2'-C3'-C4'), &nu₃ (C2'-C3'-C4'-O4'), and &nu₄ (C3'-C4'-O4'-C1'); and (iii) Pseudorotation parameters - the phase angle and amplitude of pseudorotation, P and m, derived from the sugar-ring torsions to describe the puckering of the sugar ring.

The base-pair option allows the user to access three sets of conformational parameters commonly used to characterize such interactions: (i) Hydrogen bonds - the identities and lengths of the H bonds; (ii) Local base-pair parameters - the six rigid-body parameters that relate local coordinate frames embedded on the interacting bases; and (iii) Virtual base-pair parameters - the virtual distances and angles between selected atoms on the bases and attached sugars. The set of H bonds includes the interactions between the flagged bases as well as those with the sugar-phosphate backbone and the bifurcated (three-center) H-bonds between contacted residues. The base-pair parameters- three angles called Buckle, Propeller, and Opening and three distances called Shear, Stretch, and Stagger (15) - follow the matrix-based definitions originated by Zhurkin et al. (16) and described in detail by El Hassan and Calladine (17). The virtual parameters include the distances d(C1'---C1') between the C1' atoms attached to paired bases and the angles formed by the C1'---C1' with the R(C1'-N9) or Y(C1'-N1) glycosidic bonds.

The base-pair step options allow the user to accesss ive sets of conformation parameters associated with a base-pair step: (i) Step classification - the displacement of the phosphorus atoms on interacting strands along the local dimeric and helical coordinate frames, and the conformation of the step deduced from these values. The coordinate frames on the bases, base pairs, and base-pair steps follow established conventions (18); (ii) Stacking overlap area - the area of overlap of the stacked base pairs; (iii) Base-pair step parameters - the six rigid-body parameters specifying the orientation and displacement of the constituent base pairs; (iv) Base-pair helical parameters - the six local helical parameters relating the positions of the base pairs; and (v) Virtual parameters - the distances d_(C1'-C1') between C1' atoms on successive nucleotides. The six base-pair-step parameters - three rotations (Tilt, Roll, Twist) and three translations (Shift, Slide, Rise) (15) - are the dimeric analogs of the six base-pair parameters (16,17). The six local helical parameters - Inclination, Tip, Helical Twist, x-displacement, y-displacement, Helical Rise (15) - are defined, following Babcock et al. (19), in terms of the single rotational operation that brings the coordinate frames on the base pairs into alignment. The base-pair overlap is the area shared by the four polygons formed by projecting the ring atoms of the bases on the mean base-pair plane (1). The stored data include the contributions to the overlap from the bases on the same and opposing strands and the corresponding values obtained for larger polygons constructed from the ring and exocyclic base atoms. The projections of the P atoms (xP, yP, zP) along the coordinate axes of the dimeric step distinguish A- from B-type DNA (7) as well as potential intermediate AB steps along the A - B conformational pathway (10). The corresponding projections along the axes of the local helical frame (xP(h), yP(h), zP(h)) distinguish the TA-like steps (1), i.e., the conformational form of DNA (20) found in complexes with the TATA-box protein and other proteins. The zP and zP(h) values are used to determine the conformational family of the dimer steps.

The conformational data also include the widths of the major and minor grooves, i.e., the long-range distances between phosphorus atoms on interacting strands that expose the respective non-H-bonded edges of Watson-Crick base pairs. The recorded values are based on the direct and refined formulations of El Hassan and Calladine (21) and are assigned to the relevant base-pair step. The direct values correspond to the distances between P{i}, the phosphorus atom on the leading strand of base-pair step i, and specific phosphorus atoms on the other strand, P{i-3} across the minor groove and P{i+4} across the major groove, typically the shortest cross-strand P---P distances in B-DNA helices. The refined values allow for the variation in helical structure that alters the identities of the atoms in closest cross-strand contact. Thus the two measures of groove width may differ markedly if the helix undergoes large distortions.

The above parameters can be queried with user-defined search criteria.

Once the parameters are selected the user is directed to other pages/links to narrow the set of parameters, if desired, to nucleotide units that fall within a specific Chemical Context, Sequence Context, and Conformational Category.

Chemical Context

Chemical fragment

The database allows the user to collect conformational parameters in the context of different chemical fragments, including: (i) Base pairs - the pair of nucleotides that constitute the specified hydrogen-bonded complex; and (ii) Base-pair steps - the dinucleotide units that associate as a miniduplex. For example, the backbone torsions associated with a base/nucleotide unit include the &alpha, &beta, and &gamma angles on the 5'-side of the sugar and the &epsilon and &zeta angles on the 3'-side. The torsions associated with a base-pair step include the &epsilon and &zeta angles associated with the first nucleotide and the &alpha, &beta, and &gamma angles associated with the second nucleotide.

Chemical modification

The database records whether the nucleotide bases are intact or chemically modified. The user can specify the type of nucleotides to include in the search.

Base-pair type

The database defines Watson-Crick pairs as A &hull T pairs with the requisite two H bonds, i.e., A(N1) &hull&hull&hull T(N3) and A(N6) &hull&hull&hull T(O4), and G &hull C pairs with the requsite three H bonds, i.e., G(N2) &hull&hull&hull C(O2), G(N1) &hull&hull&hull (N3) and G(O6) &hull&hull&hull C(N4). All other base pairs are classified as non-canonical pairs. The user can specify the type of base pairs to include in the search.

Sequence Context

Nucleotide(s)

The user can specify the types of bases, base pairs, and base-pair steps to include in the search. Options in include all or any combinations of the following bases (A, T, G, C), base pairs (A &hull T, T &hull A, G &hull C, C &hull G), and base-pair steps (AA &bull TT, AT &bull AT, AC &bull GT, AG &bull CT, TA &bull TA, TT &bull AA, TC &bull GA, TG &bull CA, CA &bull TG, CT &bull AG, CC &bull GG, CG &bull CG, GA &bull TC, GT &bull AC, GC &bull GC, GG &bull CC). Only parameters associated with the specified nucleotide(s) are retained.

Nucleotide neighbors

The database records the nucleotide surroundings of the base pairs and base-pair steps so that conformational features can be studied in diferent sequence contexts. That is, the base-pair and dimeric entries may include the identities of the base pairs that precede and follow the designated unit, thereby marking the relevant set of conformation data in the context of the trimer that contains the base pair and the tetramer than contains the dimer step. The annotation thus takes account of the base pairs and base-pair steps at the ends of helices. Thus, the user can specify the identities of the bases that flank particular chemical moieties. Only parameters associated with the specified chemical unit in the given sequential context are retained. This option allows the user to study the effects of neighboring base pairs on the local conformation of DNA.

Conformational Category

The user can also narrow the search by specifying the conformational category of base-pair steps. This action restricts the selection of parameters to the backbones and base pairs that constitute the base-pair steps of a particular conformational category, e.g., only A-DNA steps (as opposed to the structures with a given proportion or number of A-like steps, which can be chosen with the Structure Filter).

Parameters output

Sequential context of a base-pair step

The links associated with the base-pair steps in a grid-view table of parameters direct the user to a sequence context page that shows the chain identities, nucleotide positions, and H-bond interactions of each step in the table. The sequential locations of the associated bases are highlighted along the chains that comprise the structure. The number of H bonds associated with the two base pairs are shown on the map. The base-pair types - Watson-Crick type or non-canonical - are also noted.

Spatial context of a base-pair step

The context page of a base-pair step summarizes the values of all conformational parameters associated with the step in the database. Please refer to the Definitions page for the meanings for these parameters.