A5067569944- Protein Structure and Dynamics
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Microbial Natural Products and Biosynthesis
- Bacterial Genetics and Biotechnology
- Wheat and Barley Genetics and Pathology
- Cancer-related gene regulation
- Hippo pathway signaling and YAP/TAZ
- Advanced Proteomics Techniques and Applications
- Gene expression and cancer classification
- Mass Spectrometry Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Botanical Research and Chemistry
- Cellular Mechanics and Interactions
- Protein Tyrosine Phosphatases
- Cardiomyopathy and Myosin Studies
- Genomics and Chromatin Dynamics
- Microtubule and mitosis dynamics
- Connexins and lens biology
- Scientific Computing and Data Management
University of Reading
2016-2025
Université d'Évry Val-d'Essonne
2013
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2013
Genoscope
2013
Diamond Light Source
2012
Mary Lyon Centre at MRC Harwell
2012
Research Complex at Harwell
2012
University College London
2003-2005
Brunel University of London
2001-2002
University of Warwick
2000
Abstract Summary: The PSIPRED protein structure prediction server allows users to submit a sequence, perform of their choice and receive the results both textually via e-mail graphically web. user may select one three methods apply sequence: PSIPRED, highly accurate secondary method; MEMSAT 2, new version widely used transmembrane topology or GenTHREADER, sequence profile based fold recognition method. Availability: Freely available non-commercial at http://globin.bio.warwick.ac.uk/psipred/...
A number of state-of-the-art protein structure prediction servers have been developed by researchers working in the Bioinformatics Unit at University College London. The popular PSIPRED server allows users to perform secondary prediction, transmembrane topology and fold recognition. More recent include DISOPRED for dynamic disorder DomPred domain boundary prediction. These are available from our software home page http://bioinf.cs.ucl.ac.uk/software.html.
Dynamically disordered regions appear to be relatively abundant in eukaryotic proteomes. The DISOPRED server allows users submit a protein sequence, and returns probability estimate of each residue the sequence being disordered. results are sent both plain text graphical formats, can also supply predictions secondary structure provide further structural information.The accessed by non-commercial at http://bioinf.cs.ucl.ac.uk/disopred/
Abstract Background Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen grasses Blumeria graminis causes one the most important diseases cereal crops. B. is an obligate biotrophic as such has absolute requirement to suppress or avoid if it survive cause disease. Results Here we characterise a superfamily predicted be full complement Candidates for Secreted Effector Proteins (CSEPs) fungal barley parasite f.sp....
Abstract The IntFOLD server based at the University of Reading has been a leading method over past decade in providing free access to accurate prediction protein structures and functions. In post-AlphaFold2 world, models tertiary are widely available for even more targets, so there refocus community towards modelling protein-ligand interactions as well quaternary structure assemblies. this paper, we describe latest improvements IntFOLD, which maintains its competitive performance by...
In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of consisted a simple neural network which was trained combine sequence alignment score, length information energy potentials derived from threading into single score representing relationship between two proteins, as designated by CATH. incorporates PSI-BLAST searches, have jumpstarted with structural profiles FSSP, now also makes use PSIPRED...
A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study designed develop a reliable prediction using an alternative technique investigate the applicability of SVMs this type bioinformatics problem.Binary are trained discriminate between two structural classes. binary classifiers combined in several ways multi-class structure.The average three-state accuracy per (Q(3)) estimated by cross-validation be 77.07 +/- 0.26%...
The recent identification of multiple dominant mutations in the gene encoding β-catenin both humans and mice has enabled exploration molecular cellular basis function cognitive impairment. In humans, that cause a spectrum neurodevelopmental disorders have been identified. We identified de novo patients with intellectual disability, carefully characterized their phenotypes, were able to define recognizable disability syndrome. parallel, characterization chemically mutagenized mouse line...
The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions. component methods have been independently evaluated via successive blind CASP experiments continual CAMEO benchmarking project. has established its ranking as one best performing publicly available servers, based on...
Once you have generated a 3D model of protein, how do know whether it bears any resemblance to the actual structure? To determine usefulness models proteins, they must be assessed in terms their quality by methods that predict similarity native structure. The ModFOLD4 server is latest version our leading independent for estimation both global and local (per-residue) protein models. produces machine readable graphical output, providing users with intuitive visual reports on predicted tertiary...
Methods that reliably estimate the likely similarity between predicted and native structures of proteins have become essential for driving acceptance adoption three-dimensional protein models by life scientists. ModFOLD6 is latest version our leading resource Estimates Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The server integrates scores from three pure-single methods using neural network to local quality scores. Additionally, provides options...
IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The provides a simple unified interface aims to make complex protein modelling data more accessible life scientists. designed be intuitive set of quantitative data, so 3D results can viewed on single page interpreted by non-expert modellers at glance. only required input the amino acid sequence target protein. Here we describe major performance user updates server, which comprises...
Methods to reliably estimate the accuracy of 3D models proteins are both a fundamental part most protein folding pipelines and important for reliable identification best when multiple used. Here, we describe progress made from CASP12 CASP13 in field estimation model (EMA) as seen successful methods CASP13. We show small but clear progress, that is, several perform better than tested on EMA targets. Some is driven by applying deep learning residue-residue contacts prediction. select servers...
Methods for estimating the quality of 3D models proteins are vital tools driving acceptance and utility predicted tertiary structures by wider bioscience community. Here we describe significant major updates to ModFOLD, which has maintained its position as a leading server prediction global local protein models, over past decade (>20 000 unique external users). ModFOLD8 is latest version server, combines strengths multiple pure-single quasi-single model methods. Improvements have been made...
Abstract Intrinsic disorder (ID) in proteins is well-established structural biology, with increasing evidence for its involvement essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult compare performance, confounding biologists wanting make an informed choice. To address issue, the Critical Assessment protein Disorder...
Accurate models of protein tertiary structures are now available from numerous advanced prediction methods, although the accuracy each method often varies depending on specific target. Additionally, many may still contain significant local errors. Therefore, reliable, independent model quality estimates essential both for identifying errors and selecting very best further biological investigations. ModFOLD9 is a leading server detecting in produced by any method, it can accurately...
Abstract The elucidation of the domain content a given protein sequence in absence determined structure or significant homology to known domains is an important problem structural biology. Here we address how successfully delineation continuous can be accomplished using simple baseline methods, existing prediction algorithm (Domain Guess by Size), and newly developed method (DomSSEA). study was undertaken with view measuring usefulness these methods terms their application fully automatic...
Abstract Summary: The reliable assessment of the quality protein structural models is fundamental to progress bioinformatics. ModFOLD server provides access two accurate techniques for global and local prediction 3D proteins. Firstly ModFOLD, which a fast Model Quality Assessment Program (MQAP) used either single or multiple models. Secondly ModFOLDclust, more intensive method that carries out clustering per-residue assessment. Availability:...
Abstract Motivation: The accurate prediction of the quality 3D models is a key component successful protein tertiary structure methods. Currently, clustering- or consensus-based Model Quality Assessment Programs (MQAPs) are most methods for predicting model quality; however, they often CPU intensive as carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ—a novel MQAP that compares proteins without need by utilizing Q measure...
Abstract Motivation: Intrinsic protein disorder is functionally implicated in numerous biological roles and is, therefore, ubiquitous proteins from all three kingdoms of life. Determining the disordered regions presents a challenge for experimental methods so recently there has been much focus on development improved predictive methods. In this article, novel technique prediction, called DISOclust, described, which based analysis multiple fold recognition models. The DISOclust method...
The IntFOLD server is a novel independent that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind development were as follows: (i) to provide simple unified resource makes our software accessible all (ii) produce integrated output predictions can be easily interpreted. presented table summarizes results graphically via plots annotated 3D models. raw machine readable data files each set are also provided...
Abstract Background The accurate prediction of ligand binding residues from amino acid sequences is important for the automated functional annotation novel proteins. In previous two CASP experiments, most successful methods in function category were those which used structural superpositions 3D models and related templates with bound ligands order to identify putative contacting residues. However, whilst this process can be automated, visual inspection manual adjustments parameters, such as...