PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Geological map of HANSSONHORNA, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (hight differences) are accurate to approximately ±10 m.

Geological map of Geltinger Birk, western Baltic Sea, Germany

The geological structure of a Holocene sand spit system and the adjacent Weichselian glacial deposits in the northeastern part of Schleswig-Holstein have been investigated and presented in a geological map. Thin meltwater deposits overlie the glacial tills in the area of the former Beverö lsland in the west. To its north and northeast, the modern Sand spit system is present. Its basal transgression horizon is composed mainly of gravels and boulders, and directly overlie the Pleistocene deposits. Further up the succession, fine graind sands are present, in turn overlain by the coarser grained sands of the barrier bar. To the east, under the protection of the sand spit, gyttyas and peats which sometimes attain large thicknesses have been deposited under lacustrinellagoonal conditions. Closer to the shore, these sediments are covered by marine sands.

Geological map of RYGHNUTEN, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (hight differences) are accurate to approximately ±10 m.

Geological map of WORSFOLDFJELLET, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (height differences) are accurate to approximately ±10 m.

Geological map of JUCKESKAMMEN, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (hight differences) are accurate to approximately ±10 m.

Geological map of GRAMKROKEN, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (hight differences) are accurate to approximately ±10 m.

Geological map of KVITEBOTNEN, Heimefrontfjella, Antarctica (Scale 1:25,000)

Topographic data of this geological map were obtained through stereoscopic aerial photo interpretation. The photogrammetric photo flights were undertaken in 1986 by the Institut für Angewandte Geodäsie, Frankfurt. Horizontal ground control points required for aerial photo interpretation were determined by means of Doppler satellite observation during the 2nd German Neuschwabenland Expedition 1985/86. Vertical ground control points were taken from unpublished map drafts at 1:100 000 scale by Norsk Polarinstitutt, Oslo. The elevation above mean sea level was transferred to Heimefrontfjella barometrically. For this reason assertions concerning the absolute elevation (referred to sea level) are uncertain. Contours and spot heights presented on the map were obtained from the photogrammetric evaluation of the photography taken in 1986; relative elevation data (hight differences) are accurate to approximately ±10 m.

Map of Cordilleera Real Nord (Illampu)

Glacier maps 1 : 50000 exist of the glaciers around lllampu (6368 m) from surveys in 1928, 1963 and 1975, of the glaciers of IIlimani (6420 m) in 1975 and 1983, respectively. From these maps glacier changes 1928 - 1963 - 1975 - 1983 have been evaluated. Their retreat is smaller than that of corresponding glaciers in the Eastern Alps. The alpine advance that has begun in the sixties was not observed in the Cordillera Real.