OLDERADO: on-line database of ensemble representatives and domains. On Line Database of Ensemble Representatives And DOmains

Protein Science : a Publication of the Protein Society
L A Kelley, M J Sutcliffe

Abstract

In cases where the structure of a single protein is represented by an ensemble of conformations, there is often a need to determine the common features and to choose a "representative" conformation. This occurs, for example, with structures determined by NMR spectroscopy, analysis of the trajectory from a molecular dynamics simulation, or an ensemble of structures produced by comparative modeling. We reported previously automatic methods for (1) defining the atoms with low spatial variance across an ensemble (i.e., the "core" atoms) and the domains in which these atoms lie, and (2) clustering an ensemble into conformationally related subfamilies. To extend the utility of these methods, we have developed a freely available server on the World Wide Web at http:/(/)neon.chem.le.ac.uk/olderado/. This (1) contains an automatically generated database of representative structures, core atoms, and domains determined for 449 ensembles of NMR-derived protein structures in the Protein Data Bank (PDB) in May 1997, and (2) allows the user to upload a PDB-formatted file containing the coordinates of an ensemble of structures. The server returns in real time: (1) information on the residues constituting domains: (2) the structures that consti...Continue Reading

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jun 1, 1992·Protein Science : a Publication of the Protein Society·S G HybertsG Wagner
Dec 12, 1995·Biochemistry·C M Slupsky, B D Sykes
Jan 1, 1997·Protein Science : a Publication of the Protein Society·R SchmidtR B Altman

❮ Previous
Next ❯

Citations

Aug 30, 2003·Phytochemistry·Erika SvangårdPer Claeson
Feb 27, 1999·Current Opinion in Biotechnology·H M Berman
Feb 24, 2006·Biochemistry·Paul D Adams, Robert E Oswald
Jun 15, 2011·Biochemistry·Reena ChandrashekarPaul D Adams
Jun 13, 2012·Biochemistry·Deepa RajasekaranElias J Lolis
Oct 28, 2009·Nucleic Acids Research·S VelankarG J Kleywegt
Nov 4, 2010·Nucleic Acids Research·Sameer VelankarGerard J Kleywegt
Nov 24, 2011·Nucleic Acids Research·S VelankarG J Kleywegt
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Sameer Velankar, Gerard J Kleywegt
May 2, 2013·Acta Crystallographica. Section D, Biological Crystallography·Aleksandras GutmanasGerard J Kleywegt
May 1, 2007·Journal of Molecular Biology·Tine K NielsenRalf Ficner
Nov 30, 2013·Nucleic Acids Research·Aleksandras GutmanasGerard J Kleywegt
Jun 4, 2014·Protein Science : a Publication of the Protein Society·Vikas PejaverPredrag Radivojac
Feb 7, 2018·Scientific Reports·Shai AbehseraAmir Sagi
Jul 10, 2012·Nature Chemical Biology·Maria D CrespoRudi Glockshuber
Jul 24, 2013·Journal of Biomolecular NMR·Geerten W VuisterAleksandras Gutmanas
Jul 11, 2019·Journal of the Royal Society, Interface·Sophie Sacquin-Mora
Nov 28, 2012·Proteins·Pieter M S HendrickxGerard J Kleywegt
Jan 22, 2015·The Journal of Biological Chemistry·Sarah NeidelStephen C Graham
May 21, 2004·Protein Science : a Publication of the Protein Society·Vincenzo De FilippisAngelo Fontana
Dec 14, 2011·Journal of Structural and Functional Genomics·K Ganesan, S Parthasarathy
Jul 11, 2006·Nature Biotechnology·Andrew C DoxeyBrendan J McConkey
Sep 24, 2010·Bioinformatics·Alberto J M MartinSilvio C E Tosatto
May 15, 2020·Journal of Bioinformatics and Computational Biology·Muthuvel Prasath KaruppasamyParthasarathy Subbiah
Dec 22, 2000·Journal of Molecular Biology·J R Cupp-Vickery, L E Vickery
Jun 10, 2011·The Journal of Physical Chemistry. B·Katarzyna Kiraga-MotoszkoRyszard Stolarski
Jan 22, 2013·Biophysical Journal·Vytautas Gapsys, Bert L de Groot

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.