Related Experiment Video
Updated: Jun 20, 2026
07:35
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
Published on: October 11, 2018
PDBselect 1992-2009 and PDBfilter-select
1University of Applied Sciences Giessen, Bioinformatics, D-35390 Giessen, Germany.
Nucleic Acids Research
|September 29, 2009
Summary
PDBselect provides a curated list of unique protein chains from the Protein Data Bank (PDB) for unbiased statistical analysis. An online tool, PDBfilter-select, allows users to create custom protein selections.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- The Protein Data Bank (PDB) contains a vast number of protein structures.
- Unbiased statistical analysis requires representative protein chains with low sequence identity.
- PDBselect has historically provided such a curated list.
Purpose of the Study:
- To introduce PDBselect as a resource for representative protein chains.
- To highlight the growth of the PDBselect database.
- To present PDBfilter-select for user-defined data generation.
Main Methods:
- Selection of protein chains from the PDB based on low mutual sequence identity.
- Database curation and growth tracking over time.
- Development of an online service (PDBfilter-select) for customized data retrieval.
Main Results:
- PDBselect has expanded significantly, from 155 chains in 1992 to over 4500 chains by 2009.
- The PDBselect list serves as a valuable tool for unbiased statistical analyses in structural biology.
- PDBfilter-select enables users to generate specific subsets of the PDBselect data.
Conclusions:
- PDBselect is an essential resource for researchers needing non-redundant protein structural data.
- The PDBfilter-select service enhances the utility of PDBselect by allowing tailored data access.
- Continued curation and accessibility of such databases are crucial for advancing bioinformatics and structural biology research.
More Related Videos
12:23In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses
Published on: September 7, 2022
09:04Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
Published on: April 18, 2019
Related Concept Videos
01:25Active Filters
Active filters are electronic circuits that use operational amplifiers (op-amps), resistors, and capacitors to filter out unwanted frequency components from a signal. A first-order low-pass active filter is designed to pass signals with a frequency lower than a certain cutoff frequency and attenuate frequencies higher than that cutoff frequency. The transfer function for a first-order low-pass active filter is:
01:46Types of Selection
Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural selection can be directional, stabilizing, or disruptive. Directional selection favors one extreme trait and shifts the population towards that phenotype while selecting against individuals displaying alternate traits. Stabilizing selection favors an intermediate trait with a narrow range of variation. Deviation from the optimal phenotype towards an...
00:53Filtration
Filtration is a physical separation process that involves passing a suspension through a porous medium to separate solids from fluids. During filtration, solids collect on the porous medium while liquids, also collectively known as the filtrate, pass through. The filtration medium is selected based on the filtration purpose, quantity, and nature of the precipitate. The general criteria for a suitable filtering medium are that it is inert, mechanically strong, nonabsorbent toward dissolved...
01:25Dose-Response Relationship: Selectivity and Specificity
Drugs exert their therapeutic effects by interacting with receptors, enzymes, or ion channels that are present throughout the human body. The strength and duration of the interaction between a drug and its target receptor are characterized by the selectivity and specificity of the drug. Selectivity refers to a drug's strong preference for its intended target over other targets. For instance, isoprenaline, a non-selective β-adrenergic agonist, interacts with both β1- and β2-adrenergic receptors...
01:27Passive Filters
Passive filters are utilized to shape the frequency spectrum of signals across a diverse array of applications. These filters, using only passive elements like resistors (R), inductors (L), and capacitors (C), are capable of selectively allowing or blocking certain frequency ranges without the need for external power sources.
Low-Pass Filters
Low-pass filters are designed to transmit signals with frequencies lower than the cutoff frequency, ωc, and attenuate those above it. The cutoff frequency...
Low-Pass Filters
Low-pass filters are designed to transmit signals with frequencies lower than the cutoff frequency, ωc, and attenuate those above it. The cutoff frequency...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...