QMEANDisCo—distance constraints applied on model quality estimation

G Studer, C Rempfer, AM Waterhouse… - …, 2020 - academic.oup.com
Motivation Methods that estimate the quality of a 3D protein structure model in absence of an
experimental reference structure are crucial to determine a model's utility and potential …

Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein

AA Bahrami, Z Payandeh, S Khalili… - International reviews …, 2019 - Taylor & Francis
Immunoinformatics is a new critical field with several tools and databases that conduct the
eyesight of experimental selection and facilitate analysis of the great amount of immunologic …

Methods for the refinement of protein structure 3D models

R Adiyaman, LJ McGuffin - International journal of molecular sciences, 2019 - mdpi.com
The refinement of predicted 3D protein models is crucial in bringing them closer towards
experimental accuracy for further computational studies. Refinement approaches can be …

Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers

LJ McGuffin, NS Edmunds, AG Genc… - Nucleic acids …, 2023 - academic.oup.com
The IntFOLD server based at the University of Reading has been a leading method over the
past decade in providing free access to accurate prediction of protein structures and …

IntFOLD: an integrated web resource for high performance protein structure and function prediction

LJ McGuffin, R Adiyaman, AHA Maghrabi… - Nucleic acids …, 2019 - academic.oup.com
The IntFOLD server provides a unified resource for the automated prediction of: protein
tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain …

ModFOLD8: accurate global and local quality estimates for 3D protein models

LJ McGuffin, FMF Aldowsari, SMA Alharbi… - Nucleic acids …, 2021 - academic.oup.com
Methods for estimating the quality of 3D models of proteins are vital tools for driving the
acceptance and utility of predicted tertiary structures by the wider bioscience community …

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

J Haas, A Barbato, D Behringer… - Proteins: Structure …, 2018 - Wiley Online Library
Every second year, the community experiment “Critical Assessment of Techniques for
Structure Prediction”(CASP) is conducting an independent blind assessment of structure …

Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent

D Storey, A McNally, M Åstrand… - PLoS …, 2020 - journals.plos.org
Klebsiella pneumoniae is recognized as an urgent threat to human health due to the
increasing isolation of multidrug resistant strains. Hypervirulent strains are a major concern …

Building structural models of a whole mycoplasma cell

M Maritan, L Autin, J Karr, MW Covert, AJ Olson… - Journal of molecular …, 2022 - Elsevier
Building structural models of entire cells has been a long-standing cross-discipline
challenge for the research community, as it requires an unprecedented level of integration …

Estimation of model accuracy in CASP13

J Cheng, MH Choe, A Elofsson, KS Han… - Proteins: Structure …, 2019 - Wiley Online Library
Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental
part of most protein folding pipelines and important for reliable identification of the best …