mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/.

The Corogal: one of the big dredges in Culebra Cut, Panama Canal (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

First U.S. battleships through Panama Canal: Missouri, Ohio, Wisconsin (postcard ca 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Tow boat fleet at Paraiso, Panama Canal (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Panama Beach

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida. Photo caption: The tide rises 20 feet at high tide; at low tide the boats are used as stores to market goods.

View of Paraiso Yard showing dredging equipment, Panama Canal. (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Emergency dam at Pedro Miguel, Panama Canal (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Berm cranes at Miraflores Locks

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida. Photo notation: These are most economical in handling concrete but not so elastic as the cable way method (ca. 1914)

Lantern spillway and hydroelectric plant, Panama Canal (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

U.S.S. Ohio, Panama Canal (ca. 1914)

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

The Panamal Canal: general information

Leonard Carpenter Panama Canal Collection. Photographs: Dredging, Soldiers, and Ships. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida. (1 pamphlet; 15 pages)

View of Canal.

Leonard Carpenter Panama Canal Collection. Photographs: Views of Panama and the Canal. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

View of the Canal.

Leonard Carpenter Panama Canal Collection. Photographs: Views of Panama and the Canal. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Stone bridge in Panama.

Leonard Carpenter Panama Canal Collection. Photographs: Views of Panama and the Canal. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.

Old Timers Reunion 1928

Leonard Carpenter Panama Canal Collection. Photographs: Views of Panama and the Canal. [Box 1] from the Special Collections & Area Studies Department, George A. Smathers Libraries, University of Florida.