Entries are automatically classified by category, for example: related to cancer, have binding data available, etc. The algorithm is expected to make some errors. Please vote - in particular when you see errors in automatic classification.
Your vote is used to tag the entry and improve classification of other untagged entries. After the vote is cast for one category, such as "Cancer related", it takes 1-2 minutes for the algorithm to update the classification of all entries in PepBank. If the votes are cast for all existing categories, it takes less than 10 minutes to complete all classification for all categories. Because of this very dynamic nature, the accuracy of the classification continuously improves. Your vote is important - it helps improve classification results for this and other entries in PepBank. Do not repeatedly click the same voting button to cast the same vote many times - firstly, the extra votes are removed regularly during the QA process, and secondly, the offending IP addresses are banned from voting.
The categories are largely self-explanatory. The rules, comments and examples below provide a guide for voting.
|Short name||Category description||Vote: Yes/No||Example PMID||Example sentence||Voting Rules / Comments|
|CA||Cancer related||Yes||11026536||The antiangiogenic activity of DJS811 suggests that it may have antitumor activity as well. In addition, because SSTR2 is overexpressed on many types of tumors, DJS631 and DJS811 may be useful in the development of agents for tumor imaging or the radiotherapy of cancer.||To vote for this category, answer the question: Is the abstract directly related to the general topic of cancer (tumor cells, carcinomas, adenomas, malignancies, metastases, neoplasms, tumorogenic substances, antitumor agents, antiproliferative drugs, chemotherapy all belong here). This abstract provides a good example of a "yes" answer to this question.|
|CA||Cancer related||No||15302675||Concentrations of tumour necrosis factor-alpha (TNF-alpha) were elevated in BAL fluid from thrombin-treated mice.||Here, "tumour" is related to tumour necrosis factor-alpha (the protein), rather than directly to the topic of cancer.|
|CVD||Cardiovascular disease related||Yes||10336514||Angiotensin I-converting enzyme (ACE) is a zinc metallopeptidase that plays a major role in blood pressure regulation.||To vote for this category, answer the question: Is the abstract directly related to the general topic of cardiovascular disease ("artery disease", "blood pressure regulation", "elevated blood cholesterol", hypercholesterolemia, "valve disease", arrhythmias, atherosclerosis, hypertension, stroke all belong here). This abstract provides a good example of a "yes" answer to this question.|
|CVD||Cardiovascular disease related||No||10429241||Finally, we show that CTTHWGFTLC-displaying phage specifically target angiogenic blood vessels in vivo.||Related to blood vessels, but not directly related to cardiovascular disease.|
|DM||Diabetes related||Yes||10078546||Several recent studies have indicated that the Fas-Fas ligand system may be critical for pancreatic beta-cell destruction in type 1 diabetes.||To vote for this category, answer the question: Is the abstract directly related to the general topic of diabetes (prediabetes, antidiabetic agents, Islets of Langerhans, beta cells all belong here). This abstract provides a good example of a "yes" answer to this question.|
|DM||Diabetes related||No||11018725||Plasma from a patient with chronic pancreatic pseudocyst showed an additional more negative albumin band (18%) on agarose gel electrophoresis.||Pancreatic pseudocysts are not related to diabetes, and are usually complications of pancreatitis.|
|APO||Apoptosis related||Yes||10078546||Although the fundamental roles of caspases in the mammalian apoptotic machinery have been elucidated, it is not known which caspase or caspases play a major role in Fas-mediated apoptosis of beta-cells.||To vote for this category, answer the question: Is the abstract directly related to the general topic of apoptosis (programmed cell death, proapoptosis, antiapoptotic agents all belong here). This abstract provides a good example of a "yes" answer to this question.|
|APO||Apoptosis related||No||7768361||Nanomolar concentrations of a 22-mer peptide encompassing this region stimulated neurite outgrowth and choline acetyltransferase activity, and prevented cell death in neuroblastoma cells.||"Cell death" is not necessarily "programmed cell death", and thus not directly related to apoptosis.|
|ANG||Angiogenesis related||Yes||11026536||The antiangiogenic activity of DJS811 suggests that it may have antitumor activity as well.||To vote for this category, answer the question: Is the abstract directly related to the general topic of angiogenesis (antiangiogenesis, arteriogenesis, neovascularization, vessel formation, antiangiogenic agents all belong here). This abstract provides a good example of a "yes" answer to this question.|
|ANG||Angiogenesis related||No||16547525||The present study further demonstrated that the use of high signal transduction/coupling efficiency isolated blood vessel assays (primate greater than cat arteries) is required in order to characterize UT receptor antagonism thoroughly.||Related to blood vessels, but not to the growth of new blood vessels (angiogenesis)|
|MI||Molecular imaging related||Yes||11026536||In addition, because SSTR2 is overexpressed on many types of tumors, DJS631 and DJS811 may be useful in the development of agents for tumor imaging or the radiotherapy of cancer.||To vote for this category, answer the question: Is the abstract directly related to the general topic of molecular imaging (PET, SPECT, MRI, fluorescence, luminescence all belong here). This abstract provides a good example of a "yes" answer to this question.|
|MI||Molecular imaging related||No||8364157||Proton magnetic resonance studies of bradykinin antagonists. [...] Conformational studies based on two-dimensional nmr experiments in methanol/water (80/20 v/v) were carried out on several such active antagonists in a polar solvent.||Nuclear magnetic resonance in this context (structural biology) is not directly related to molecular imaging (but MRI is).|
|BD||Binding data available||Yes||10496948||Dissociation constants were in the 10 microM range.||To vote for this category, answer the question: Does the abstract provide any numeric data that tells us something about binding (affinity, activity, some kind of effect - anything where concentration is factored in) of any entities, in absolute (rather than relative) units? This abstract provides a good example of a "yes" answer to this question.|
|BD||Binding data available||Yes||6373590||In vitro, the ID50 needed to inhibit both dog and human plasma renin is approximately 10(-8)M.||The data on affinity or activity can be expressed differently. For example, deltaG, Ka, Kd, Km, EC50, IC50, GI50, ID90, LD50, MIC90, pKd, etc are all okay. The units can vary as well, for example mol/L, nanoM, mg/ml, mg/kg, cells/L, etc. Note that common abbreviations may mean different things: mol can be mole or mole/liter, mm can be millimeter or millimole/liter, etc.|
|BD||Binding data available||Yes||16409474||At 50 s(-1), alpha(IIb)beta3 T562N supported higher cell adhesion to fibrinogen (63.3 +/- 2.9 cells/field)||Provides some numeric data about binding, even though not in proper concentration units.|
|BD||Binding data available||No||2844270||Rabbit liver phosphofructo-1-kinase, designated isozyme B, and rabbit brain phosphofructokinase, which contains all three isozymes as heteropolymers, have been modified by [14C]fluorosulfonylbenzoyladenosine (FSBAdo). [...] The modification proceeded to the extent of 2 to 4 mol of reagent incorporated per mol of tetramer.||These are data on stoichiometry, not on binding/activity/concentration.|
|BD||Binding data available||No||11724584||The subsequent formation of a trigonal thiolato Hg(II) in the interior of a three-stranded coiled coil was verified by the presence of a characteristic HgS(3) UV band at 248 nm.||Here, nm = nanometers, not nanomolar|
|BD||Binding data available||No||16259560||Two rounds of screening on primary tumors yielded multiple copies of a phage that displays a cyclic 7-amino acid peptide, SRESPHP, with a 3000-fold increase in titer between rounds 1 and 2. The selected phage showed highly specific binding to the tumor after systemic administration, whereas binding to other organs such as lung, liver, kidney, and heart was reduced up to 90%.||Binding data are relative, not absolute. They tell us nothing about, for example, the Kd.|
AccNo - interaction accession number.
Score - overall confidence score. It is a measure of confidence of the entry, taking into account peptide sequence text mining (if the sequence was mined from text) and the annotation quality (if the sequence was manually annotated). It is not related to automatically classifying the entry into different categories, such as cancer, angiogenesis, etc. The score ranges from 0 (lowest) to 1 (highest). The score is higher for manually annotated than for automatically mined entries:
Name - interaction short name.
Environment - where the interaction takes place. Example: in vitro.
Kd - dissociation constant (M), 1.0 if data are not available.
Organism - where the interaction takes place (can be different from peptide and interactor organism, see below).
Function - interaction function.
AccNo - peptide accession number.
Name - peptide short name.
Description - peptide description.
Organism - peptide organism, for synthetic peptides: 'N/A'.
Constraint - peptide conformational constraint. Example: disulfide.
Sequence - peptide sequence or motif, in 1 letter symbols.
Origin - peptide origin. Examples: phage display, natural.
Form - form of the peptide. Examples: phage, synthetic.
Internalized - is the peptide internalized into cells? yes/no.
Unnatural - unnatural amino acids. Example: D-amino acids.
Imaging - imaging use of the peptide. Examples: PET, MRI.
Is Motif - is the peptide a motif? yes/no. Examples of motifs: RGD - a consensus motif for sequences RGDA, RGDL and KRGD; RGD(A/L) - a consensus motif for sequences RGDA, RGDL. Examples of sequences: RGD (an individual synthetic tripeptide), RGDA, RGDL.
AccNo - interactor accession number.
Name - interactor short name.
Description - interactor description.
Organism - interactor organism.
Type - interactor. Examples: protein, cell.
AccNo - experiment accession number.
Name - experiment short name.
Detection - interaction detection method, describes the method by which the interaction was identified. See Proteomics Standards Initiative Molecular Interaction XML Format Documentation
Source - experiment data source. Examples: PubMed, UniProt, ASPD.
Text Id - text identifier, such as a UniProt accession number or a PubMed id. Examples: P61298, 14759804.
Journal - article citation: journal, year, volume, pages.
Title - article title.
Authors - article authors.
Text - abstract text, with peptide sequences in red.