Abstract:
BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. RESULTS:Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets. According to the presented benchmarks, the newly developed IPC pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Moreover, the prediction of pI using the IPC pKa's leads to fewer outliers, i.e., predictions affected by errors greater than a given threshold. CONCLUSIONS:The IPC service is freely available at http://isoelectric.ovh.org Peptide and protein datasets used in the study and the precalculated pI for the PDB and some of the most frequently used proteomes are available for large-scale analysis and future development. REVIEWERS:This article was reviewed by Frank Eisenhaber and Zoltán Gáspári.
journal_name
Biol Directjournal_title
Biology directauthors
Kozlowski LPdoi
10.1186/s13062-016-0159-9subject
Has Abstractpub_date
2016-10-21 00:00:00pages
55issue
1issn
1745-6150pii
10.1186/s13062-016-0159-9journal_volume
11pub_type
杂志文章相关文献
Biology Direct文献大全abstract:BACKGROUND:The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Del...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-5-61
更新日期:2010-11-02 00:00:00
abstract:UNLABELLED:Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the for...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-5-17
更新日期:2010-04-12 00:00:00
abstract:UNLABELLED:Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true f...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-38
更新日期:2009-10-06 00:00:00
abstract:BACKGROUND:Glycogen synthase kinase-3 (GSK-3) is a ubiquitously expressed serine/threonine (Ser/Thr) kinase comprising two isoforms, GSK-3α and GSK-3β. Both enzymes are similarly inactivated by serine phosphorylation (GSK-3α at Ser21 and GSK-3β at Ser9) and activated by tyrosine phosphorylation (GSK-3α at Tyr279 and GS...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-4
更新日期:2011-01-24 00:00:00
abstract:BACKGROUND:The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-24
更新日期:2011-05-18 00:00:00
abstract:BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-7-32
更新日期:2012-09-26 00:00:00
abstract:BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-018-0221-x
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-14
更新日期:2011-02-22 00:00:00
abstract:UNLABELLED:In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...
journal_title:Biology direct
pub_type: 杂志文章,评审
doi:10.1186/s13062-016-0142-5
更新日期:2016-08-23 00:00:00
abstract::Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses o...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-015-0047-8
更新日期:2015-03-29 00:00:00
abstract:BACKGROUND:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-018-0225-6
更新日期:2018-10-12 00:00:00
abstract:BACKGROUND:Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion. RESULTS:Comparisons...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-9
更新日期:2009-02-26 00:00:00
abstract:BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-8-17
更新日期:2013-07-08 00:00:00
abstract:BACKGROUND:Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological information about the underlying metabolic networks. These networks have been shown to share domain-...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-53
更新日期:2011-10-13 00:00:00
abstract::tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified th...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-8-6
更新日期:2013-02-12 00:00:00
abstract::Shannon entropy is used to provide an estimate of the number of interpretable components in a principal component analysis. In addition, several ad hoc stopping rules for dimension determination are reviewed and a modification of the broken stick model is presented. The modification incorporates a test for the presenc...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-2-2
更新日期:2007-01-17 00:00:00
abstract:BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-2-4
更新日期:2007-01-24 00:00:00
abstract:BACKGROUND:H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homolo...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-9-5
更新日期:2014-04-08 00:00:00
abstract:BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-1-28
更新日期:2006-09-13 00:00:00
abstract:BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-9-23
更新日期:2014-11-18 00:00:00
abstract:UNLABELLED:Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via ar...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-3-45
更新日期:2008-11-03 00:00:00
abstract:BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-018-0209-6
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the ta...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-29
更新日期:2009-08-25 00:00:00
abstract:BACKGROUND:The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequen...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-016-0120-y
更新日期:2016-04-07 00:00:00
abstract:BACKGROUND:Microscopic examination of living cells often reveals that cells from some cell strains appear to be in a permanent state of disarray without obvious reason. In all probability such a disorderly state affects cell functioning. The aim of this study was to establish whether a disorderly state could occur that...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-1-9
更新日期:2006-04-02 00:00:00
abstract:BACKGROUND:The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. CONCEPT:Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-33
更新日期:2009-09-29 00:00:00
abstract:BACKGROUND:The transition from premalignant to invasive tumour growth is a prolonged multistep process governed by phenotypic adaptation to changing microenvironmental selection pressures. Cancer prevention strategies are required to interrupt or delay somatic evolution of the malignant invasive phenotype. Empirical st...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-5-22
更新日期:2010-04-20 00:00:00
abstract:BACKGROUND:In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natur...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-015-0103-4
更新日期:2015-12-21 00:00:00
abstract::Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the s...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-020-00260-9
更新日期:2020-04-28 00:00:00
abstract:BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-7-12
更新日期:2012-04-17 00:00:00