Three-dimensional protein structure prediction: Methods and computational strategies

M Dorn, MB e Silva, LS Buriol, LC Lamb - Computational biology and …, 2014 - Elsevier
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

RM Bennett‐Lovsey, AD Herbert… - Proteins: Structure …, 2008 - Wiley Online Library
Structural and functional annotation of the large and growing database of genomic
sequences is a major problem in modern biology. Protein structure prediction by detecting …

QMEAN server for protein model quality estimation

P Benkert, M Künzli, T Schwede - Nucleic acids research, 2009 - academic.oup.com
Abstract Model quality estimation is an essential component of protein structure prediction,
since ultimately the accuracy of a model determines its usefulness for specific applications …

LOMETS: a local meta-threading-server for protein structure prediction

S Wu, Y Zhang - Nucleic acids research, 2007 - academic.oup.com
We developed LOMETS, a local threading meta-server, for quick and automated predictions
of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs …

Can correct protein models be identified?

B Wallner, A Elofsson - Protein science, 2003 - Wiley Online Library
The ability to separate correct models of protein structures from less correct models is of the
greatest importance for protein structure prediction methods. Several studies have examined …

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

J Hou, T Wu, R Cao, J Cheng - Proteins: Structure, Function …, 2019 - Wiley Online Library
Predicting residue‐residue distance relationships (eg, contacts) has become the key
direction to advance protein structure prediction since 2014 CASP11 experiment, while …

GraphQA: protein model quality assessment using graph convolutional networks

F Baldassarre, D Menéndez Hurtado, A Elofsson… - …, 2021 - academic.oup.com
Motivation Proteins are ubiquitous molecules whose function in biological processes is
determined by their 3D structure. Experimental identification of a protein's structure can be …

3D-Jury: a simple approach to improve protein structure predictions

K Ginalski, A Elofsson, D Fischer, L Rychlewski - Bioinformatics, 2003 - academic.oup.com
Motivation: Consensus structure prediction methods (meta-predictors) have higher accuracy
than individual structure prediction algorithms (their components). The goal for the …

ProQ3D: improved model quality assessments using deep learning

K Uziela, D Menéndez Hurtado, N Shu, B Wallner… - …, 2017 - academic.oup.com
Protein quality assessment is a long-standing problem in bioinformatics. For more than a
decade we have developed state-of-art predictors by carefully selecting and optimising …

GeneSilico protein structure prediction meta-server

MA Kurowski, JM Bujnicki - Nucleic acids research, 2003 - academic.oup.com
Rigorous assessments of protein structure prediction have demonstrated that fold
recognition methods can identify remote similarities between proteins when standard …