A5011869206- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Bacteriophages and microbial interactions
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Transgenic Plants and Applications
- PI3K/AKT/mTOR signaling in cancer
- Cellular transport and secretion
- Fungal and yeast genetics research
- Monoclonal and Polyclonal Antibodies Research
- Protein Kinase Regulation and GTPase Signaling
- Ubiquitin and proteasome pathways
- Cancer-related gene regulation
- Microbial Metabolic Engineering and Bioproduction
- Microtubule and mitosis dynamics
- Wnt/β-catenin signaling in development and cancer
- Mass Spectrometry Techniques and Applications
- Influenza Virus Research Studies
Nanjing Tech University
2025
Chongqing University
2024
Shenyang University of Technology
2006-2022
University of South Florida
2011-2020
China University of Mining and Technology
2017
USF Health Byrd Alzheimer's Institute
2016
Sichuan University
2015
Indiana University – Purdue University Indianapolis
2007-2014
Indiana University School of Medicine
2007-2014
Florida State University
2014
We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results predicted (mostly structured) SCOP domains using SUPERFAMILY predictor. These disorder/structure annotations together enable...
Intrinsically disordered proteins and intrinsically protein regions are highly abundant in nature. However, the quantitative qualitative measures of intrinsic disorder species with known genomes still not available. Furthermore, although correlation between high fraction residues advanced has been reported, details this connection content proteome complexity have reported as yet. To fill gap, we analysed entire proteomes 3484 from three domains life (archaea, bacteria eukaryotes) viruses....
Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered that bind to protein partners via disorder-to-order transitions. MoRFs implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated is known, which motivates development computational methods predict from chains.We introduce new MoRF predictor, MoRFpred, identifies all types (α, β, coil complex). We develop...
Intrinsically disordered proteins (IDPs) and intrinsically regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs IDRs is leading to an entire field aimed at their systematic structural characterization determination mechanisms action. Bioinformatics studies showed that are highly abundant in different proteomes carry out mostly regulatory functions related molecular signal transduction. These activities complement...
Molecular recognition features (MoRFs) are intrinsically disordered protein regions that bind to partners via disorder-to-order transitions. In one-to-many binding, a single MoRF binds two or more different individually. MoRF-based protein-protein interaction (PPI) examples were collected from the Protein Data Bank, yielding 23 MoRFs bound 2-9 partners, with all pairs of same-MoRF having less than 25% sequence identity. Of these, 8 completely folds, whereas 15 2-5 same folds but low...
Abstract Short and long disordered regions of proteins have different preference for amino acid residues. Different methods often to be trained predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes three-state prediction first (ordered residues in short regions) reduces it into two-state afterwards. was tested on various sets composed combinations Disprot annotated directly from the PDB disorder by missing coordinates X-ray...
Many proteins or their regions known as intrinsically disordered (IDPs) and (IDRs) lack unique 3D structure in native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs IDRs are highly abundant different proteomes carry out mostly regulatory functions related to molecular recognition signal transduction. Archaea belong an intriguing domain of life whose members, being microbes, characterized by a mosaic-like combination...
Many biologically active proteins are intrinsically disordered. A reasonable understanding of the disorder status these may be beneficial for better their structures and functions. The contents disordered vary dramatically, with two extremes being fully ordered proteins. Often, it is necessary to perform a binary classification classify whole protein as or Here, an improved error estimation technique was applied develop cumulative distribution function (CDF) algorithms several established...
Many biologically active proteins are disordered as a whole, or contain long regions. These intrinsically proteins/regions very common in nature, abundantly found all organisms, where they carry out important biological functions. The functions of these complement the functional repertoire "normal" ordered proteins, and many protein classes heavily dependent on intrinsic disorder. Among disorder-centric interactions with nucleic acids complex assembly. In this study, we present results...
Abstract This article attempts to increase the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles proteins through improved learning. Most methods developed for improving backpropagation algorithm artificial neural networks are limited small networks. Here, we introduce a guided‐learning method suitable any size. The employs part weights guiding other training optimization. We demonstrate this technique by predicting proteins. In application, factor...
We analysed the structural properties of protein regions containing arrays perfect and nearly tandem repeats. Naturally occurring proteins with repeats are practically absent among known 3D structures. The great majority such in Protein Data Bank found designed de novo . abundance natural structured is inversely correlated repeat perfection: chance finding increases a decrease level perfection. Prediction intrinsic disorder within SwissProt supports conclusion that perfection correlates...
We analysed the structural properties of protein regions containing arrays perfect and nearly tandem repeats. Naturally occurring proteins with repeats are practically absent among known 3D structures. The great majority such in Protein Data Bank found designed de novo. abundance natural structured is inversely correlated repeat perfection: chance finding increases a decrease level perfection. Prediction intrinsic disorder within SwissProt supports conclusion that perfection correlates their...
IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) elucidated the molecular principles which its region (IDR) at carboxyl-terminus (C-tail) executes functions. Post-translational modifications, conserved eukaryotic linear motifs recognition features present C-tail IDR enhance PTEN's...
The earliest whole protein order/disorder predictor (Uversky et al., Proteins, 41: 415-427 (2000)), herein called the charge-hydropathy (C-H) plot, was originally developed using Kyte-Doolittle (1982) hydropathy scale (Kyte & Doolittle., J. Mol. Biol, 157: 105-132(1982)). Here goal is to determine whether performance of C-H plot in separating structured and disordered proteins can be improved by an alternative scale.Using CH-plot as metric, we compared 19 scales, with finding that Guy (1985)...