SUMMARY InterMap3D predicts co-evolving protein residues and plots them on the 3D protein structure. Starting with a single protein sequence, InterMap3D automatically finds a set of homologous sequences, generates an alignment and fetches the most similar 3D structure from the Protein Data Bank (PDB). It can also accept a user-generated alignment. Based on the alignment, co-evolving residues ar...

Methods: Structure of DNA gyrase (2XCT) was retrieved from the Protein Data Bank (PDB) and the structures of (FQ) compounds were selected from literature survey of 400 novel compounds and the physical, chemical and molecular characteristics of each compound were obeyed for drugrelevant properties based on “Lipinski’s rule of five, then a total of 150 (FQ)s were docked against the protein of the...

The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallizatio...

The Protein Data Bank (PDB) is a widely used biological database of macromolecular structures with a long history. This history is treated as lessons learned and is used to highlight what are believed to be the best practices important to developers of biological databases today. While the focus is on data quality, data representation and the information technology to support these data, the no...

PDBselect (http://bioinfo.tg.fh-giessen.de/pdbselect/) is a list of representative protein chains with low mutual sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. The list increased from 155 chains in 1992 to more than 4500 chains in 2009. PDBfilter-select is an online service to generate user-defined selections.

A primary function of the Intelligence Community (IC) is to support the president, the National Security Council, and other top government leaders. The most well-known example of this support is the President’s Daily Briefing (PDB). The PDB—as reflected in actual printed products and the person-to-person interactions between PDB recipients and intelligence briefers—has evolved over the decades ...

PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were predetermined, on the WWW. The current version is designed so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configur...

UNLABELLED A WWW server is described for creating 3D models of canonical or bent DNA starting from sequence data. Predicted DNA trajectory is first computed based on a choice of di- and tri-nucleotide models (M.G. Munteanu et al., Trends Biochem. Sci. 23, 341-347, 1998); an atomic model is then constructed and optionally energy-minimized with constrained molecular dynamics. The data are present...

SUMMARY A web-based three-dimensional (3D) protein retrieval system is available for protein structure data including all PDB and FSSP dataset. In this system, we use a visual-based matching method to compare the protein structure from multiple viewpoints. It takes less than three seconds for each query with 90% accuracy on an average.

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some more than 30 years old, were constructed with methods of their era. With PDB_REDO we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystal...