Degpred
Degrons are short linear motifs, bound by E3 ubiquitin ligases to target proteins to be degraded by the ubiquitin-proteasome system. Deregulation of degron disrupts control of protein abundance and commonly contributes to diseases. Despite with important functions, only a limited number of degrons have been identified by experiment, the widely used motif matching prediction method is limited by few motifs and high false positive rate. Here, we developed a deep learning model Degpred to predict degrons directly from protein sequences. Leveraging abundant protein features provided by the BERT based model, Degpred predicts degrons beyond those from known motifs and greatly expands the degron landscape. Degpred outperformed motif-based methods in capturing well-known degron properties. Furthermore, we calculated motifs for 39 E3s using our collected E3-substrate interaction dataset and assigned predicted degrons to specific E3s. In summary, we presented an efficient and general tool to predict degrons and binding E3s, both collected and predicted datasets were integrated in this website.
PhaSePred
Phase
separation (PS) is driven by multivalent weak interactions mediated by intrinsically disordered
regions (IDRs) or multiple modular domains. A difference between these two interactions is
that a single molecule species can undergo IDR-mediated phase separation, while phase
separation mediated by multiple interacting domains often involves two or more different
molecule species. Herein, we characterize proteins that can self-assemble to form
condensates as self-assembling phase-separating (PS-Self) proteins, and we define proteins
whose phase separation behaviors are regulated by partner components (proteins or nucleic
acids) as partner-dependent phase-separating (PS-Part) proteins.
PhaSePred is a centralized resource that provides self-assembling and partner-dependent
phase-separating protein prediction and integrates scores from several PS-related predicting
tools.
MloDisDB
Membraneless
organelles (MLOs) play important roles in the temporal and spatial regulation of various
biological processes, and emerging evidence supports that liquid-liquid phase separation
(LLPS) is underlying the assembly of MLOs. Dysfunction of MLOs and LLPS are associated with
various pathological processes.
MloDisDB aims to gather MLOs and LLPS related diseases
from the dispersed literature. Each entry was assigned with one of the three evidence levels
based on original publication: Direct experiment, Indirect experiment, Clinical
Investigation. The functional factors, changes of MLOs and changes of the factors were
recorded, the components of MLOs and LLPS related predictions were integrated.
PhaSepDB
PhaSepDB
provides a collection of manually curated phase separation (PS) proteins and Membraneless
organelles (MLOs) related proteins. As of June 2021, 961 PS entries, 59 MLOs, 698 low
throughput MLO related entries and 6981 high throughput MLO related entries were
included.
PS entries were classified into 356 “PS-self” (the protein can undergo PS in
vitro by itself) and 605 “PS-other” entries (the protein require other partners to form
biomolecular droplet in vitro or can form or be recruited to biomolecular droplet in
vivo).
We provide detailed annotation for many PS entries, including the material states
of the PS droplets, the regions used in experiments, PS partners for the proteins and the
regulation of the proteins' PS ability.
ASEB
Lysine acetylation is one of the important post-translational modifications of both histone and non-histone proteins. Thousands of acetylated proteins are known. ASEB is a web server to predict novel KAT-specific acetylated sites or HADC-specific deacetylated sites based on the different characteristics. Here, we provide two methods to make prediction: (1) one method is merely using protein sequence information based on statistic analysis; (2) the other method is utilizing protein sequence and functional features based on machine learning and statistic analysis. Please click the link below for details.
PTM-X
Protein post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions. Many PTM sites from the same (intra) or different (inter) proteins are not isolated, and instead may coordinate with each other to determine a functional outcome, which is defined as PTM cross-talk. PTM-X is a web server to predict PTM cross-talk both intra- and inter- protein. Please click the link below for details.
lncpro
This is a website for predicting the interaction between long noncoding RNAs and proteins. By coding RNA and protein sequences into vectors, we use matrix multiplication to give score to each RNA-protein pair. This score can be the measurement of interactions between the RNA-protein pair. Comparing to existing approaches, this method shortens the time for training matrix. It also theoretically guarantees the results to be the best solution. The method has shown good ability to discriminate interacting/non-interacting RNA-protein pairs and to predict the RNA-protein interaction within a given complex. Please click the link below for details.
ptpset
Ptpset is a webserver to make prediction of human potential phosphorylation substrates. Here, the prediction method mainly uses protein sequence information and is designed based on KNN algorithm. Substrates of three kinases (PTP1B/SHP-1/SHP-2) can be predicted now. Users have two choices to set the prediction cutoff (low/high). Please click the link below for details.
hUbiquitome
Protein ubiquitination is an evolutional conserved and functional diversity posttranslational modification which is achieved through the sequential action of E1 activating enzymes, E2 conjugating enzymes, and E3 ligases.Here, we introduce a web resources hUbiquitome which is a public resource for the retrieval of experimentally verified human ubiquination enzymes and substrates. It is the first comprehensive database of human ubiqutitination pathway proteins and ubiquitin binding-site sequences which is freely available to academia. hUbiquitome: A database of experimentally verified ubiquitination cascades in human. Please click the link below for details.
phospho
Protein phosphorylation is a kind of post-translational modification which plays key roles in many cellular processes. Detection of possible phosphorylation sites of a protein is important for understanding the protein function.Here we integrate information such as protein functional domains, protein subcellular location and protein-protein interactions, along with the polypeptide sequences to predict phosphorylation sites. We scanned a set of human proteins collected from Swiss-Prot and predicted putative phosphorylation sites for Cyclin-dependent kinases, Casein kinase 2, Glycogen synthase kinase 3, Mitogen-activated protein kinases, protein kinase A and protein kinase C families. Please click the link below for details.
