Protein structure prediction in casp13 using awsem-suite

S Jin, M Chen, X Chen, C Bueno, W Lu… - Journal of chemical …, 2020 - ACS Publications
Recently several techniques have emerged that significantly enhance the quality of
predictions of protein tertiary structures. In this study, we describe the performance of …

AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes

S Jin, VG Contessoto, M Chen, NP Schafer… - Nucleic acids …, 2020 - academic.oup.com
The accurate and reliable prediction of the 3D structures of proteins and their assemblies
remains difficult even though the number of solved structures soars and prediction …

Template-guided protein structure prediction and refinement using optimized folding landscape force fields

M Chen, X Lin, W Lu, NP Schafer… - Journal of chemical …, 2018 - ACS Publications
When good structural templates can be identified, template-based modeling is the most
reliable way to predict the tertiary structure of proteins. In this study, we combine template …

Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model

SM Gopal, K Klenin, W Wenzel - Proteins: Structure, Function …, 2009 - Wiley Online Library
Biophysical forcefields have contributed less than originally anticipated to recent progress in
protein structure prediction. Here, we have investigated the selectivity of a recently …

Protein structure prediction: Making AWSEM AWSEM‐ER by adding evolutionary restraints

BJ Sirovetz, NP Schafer… - … : Structure, Function, and …, 2017 - Wiley Online Library
Protein sequences have evolved to fold into functional structures, resulting in families of
diverse protein sequences that all share the same overall fold. One can harness protein …

DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function

JW Lee, JH Won, S Jeon, Y Choo, Y Yeon, JS Oh… - …, 2023 - academic.oup.com
Motivation Predicting protein structures with high accuracy is a critical challenge for the
broad community of life sciences and industry. Despite progress made by deep neural …

Evaluation of the template‐based modeling in CASP12

A Kryshtafovych, B Monastyrskyy… - Proteins: Structure …, 2018 - Wiley Online Library
The article describes results of numerical evaluation of CASP12 models submitted on
targets for which structural templates could be identified and for which servers produced …

Improved protein structure prediction using predicted interresidue orientations

J Yang, I Anishchenko, H Park… - Proceedings of the …, 2020 - National Acad Sciences
The prediction of interresidue contacts and distances from coevolutionary data using deep
learning has considerably advanced protein structure prediction. Here, we build on these …

Data‐assisted protein structure modeling by global optimization in CASP12

K Joo, S Heo, IS Joung, SH Hong… - Proteins: Structure …, 2018 - Wiley Online Library
In CASP12, 2 types of data‐assisted protein structure modeling were experimented. Either
SAXS experimental data or cross‐linking experimental data was provided for a selected …

TopModel: template-based protein structure prediction at low sequence identity using top-down consensus and deep neural networks

D Mulnaes, N Porta, R Clemens… - Journal of chemical …, 2020 - ACS Publications
Knowledge of protein structures is essential to understand proteins' functions, evolution,
dynamics, stabilities, and interactions and for data-driven protein-or drug design. Yet …