نتایج جستجو برای: protein data bank
تعداد نتایج: 3499249 فیلتر نتایج به سال:
Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering.
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem...
VOLUME 25 NUMBER 8 AUGUST 2007 NATURE BIOTECHNOLOGY Finally, we certainly agree that the PDB should have a standard data representation, although a well-designed ontology plays less of a role than that championed by King and his coauthors. Even so, the legacy requirements of our community and the dynamics of changing a global resource require that it be developed over time and in collaboration ...
The Protein Data Bank (PDB) [3] is the most important depository of protein structural information, containing more than 42,000 deposited entries today. Because of its inhomogeneous structure, its fully automated processing is almost impossible. In a previous work, we cleaned and re-structured the entries in the Protein Data Bank, and from the result we have built the RS-PDB database [11]. Usin...
ABSTRACT Most fully automatic information extraction systems achieve less than 100% extraction precision and recall. On real applications these parameters typically vary between 50% to 95%, depending on the extraction method and source data. We present an information extraction system designed for applications where little or no error can be tolerated. The system is not fully automatic. Instead...
Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein-protein and protein-DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein-protein and protein-DNA interactions. However, currently there is no pub...
The Protein Data Bank (PDB) contains, at least implicitly, empirical information about the bond angles between pairs of amino acids. There is considerable variation in the observed values for a given amino acid pair, and it is not clear whether this variation represents a wide range of conformal possibilities or is due to noise. We show, by applying singular value decompositions to the sets of ...
The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structure...
Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analys...
The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. C...
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