Abstract:
BACKGROUND:Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. RESULTS:Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. CONCLUSIONS:The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Pravda L,Berka K,Svobodová Vařeková R,Sehnal D,Banáš P,Laskowski RA,Koča J,Otyepka Mdoi
10.1186/s12859-014-0379-xsubject
Has Abstractpub_date
2014-11-18 00:00:00pages
379issn
1471-2105pii
s12859-014-0379-xjournal_volume
15pub_type
杂志文章abstract:BACKGROUND:Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-176
更新日期:2004-11-04 00:00:00
abstract:BACKGROUND:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-379
更新日期:2011-09-26 00:00:00
abstract:BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-55
更新日期:2004-05-07 00:00:00
abstract:BACKGROUND:Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-182
更新日期:2014-06-12 00:00:00
abstract:BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03928-1
更新日期:2020-12-17 00:00:00
abstract:BACKGROUND:Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-215
更新日期:2010-04-29 00:00:00
abstract:BACKGROUND:The structure conservation in various α-helix subclasses reveals the sequence and context dependent factors causing distortions in the α-helix. The sequence-structure relationship in these subclasses can be used to predict structural variations in α-helix purely based on its sequence. We train support vector...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S20
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03777-y
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, and the number of common predicted essential proteins by different methods is very small. RESULTS:In ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1166-7
更新日期:2016-08-25 00:00:00
abstract:BACKGROUND:Joint and individual variation explained (JIVE), distinct and common simultaneous component analysis (DISCO) and O2-PLS, a two-block (X-Y) latent variable regression method with an integral OSC filter can all be used for the integrated analysis of multiple data sets and decompose them in three terms: a low(e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1037-2
更新日期:2016-06-06 00:00:00
abstract:BACKGROUND:Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molec...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-3-34
更新日期:2002-11-01 00:00:00
abstract:BACKGROUND:Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important concepts and the identification of relationships between those concepts in patient records are preli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S3-S3
更新日期:2011-06-09 00:00:00
abstract:BACKGROUND:Periodic phenomena are widespread in biology. The problem of finding periodicity in biological time series can be viewed as a multiple hypothesis testing of the spectral content of a given time series. The exact noise characteristics are unknown in many bioinformatics applications. Furthermore, the observed ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-117
更新日期:2005-05-13 00:00:00
abstract:BACKGROUND:RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and even more so transcript counting methods which avoid mapping and quantify gene and transcript expres...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2799-0
更新日期:2019-05-03 00:00:00
abstract:BACKGROUND:Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03668-2
更新日期:2020-11-11 00:00:00
abstract:BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-255
更新日期:2013-08-21 00:00:00
abstract:BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03691-3
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-69
更新日期:2011-03-08 00:00:00
abstract:BACKGROUND:An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1865-8
更新日期:2017-10-23 00:00:00
abstract:BACKGROUND:Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the N...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-381
更新日期:2011-09-27 00:00:00
abstract:BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-480
更新日期:2008-11-13 00:00:00
abstract:BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2272-5
更新日期:2018-08-13 00:00:00
abstract:BACKGROUND:Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination spots is both time-consuming and costly. Developing an accurate and automated method for reliably and ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-340
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-S2-S3
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-323
更新日期:2009-10-08 00:00:00
abstract:BACKGROUND:Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Several approaches for sample size determination have been developed for expression array studies, but...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-331
更新日期:2010-06-17 00:00:00
abstract:BACKGROUND:Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in higher frequencies than in random networks. They have recently gathered much attention as a useful concep...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-318
更新日期:2009-10-04 00:00:00
abstract:BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2160-z
更新日期:2018-04-25 00:00:00
abstract:BACKGROUND:Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S17-S9
更新日期:2012-01-01 00:00:00
abstract::We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...
journal_title:BMC bioinformatics
pub_type:
doi:10.1186/1471-2105-9-S1-S1
更新日期:2008-01-01 00:00:00