| This is a
database of ligand binding proteins aligned to structural templates.
The structural templates are taken from the PDB
, 3D models of the aligned sequences are provided ModBase, and
pairwise sequence alignments are provided by CE. Multiple Structural Alignments are built on the fly within LigBase from a series of pairwise alignments. Ligand diagrams are generated with Andrew Wallace's program Ligplot (Wallace AC, Laskowski RA & Thornton JM (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Prot. Eng., 8, 127-134.) Ligands that are closer than 1.8 Angstroms are designated as covalent modifications but are nevertheless retained in the database.
The ModView program from
UCSF provides an excellent tool for comparative viewing of sequence and structure alignments on Linux or SGI platforms using Netscape 4.x.
The database will grow
with the availability of new sequences and structures.
All 3D structural models are calculated with automated procedures based on the MODELLER
program (Sali, A & Blundell, TL 1993. J Mol Biol 234,
For comments or suggestions:
Developed by Andrea Rossi and Ash Stuart in the Lab of Andrej Sali
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and
California Institute for Quantitative Biomedical Research
University of California San Francisco
San Francisco, CA 94143-2552