GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

GR Lee, J Won, L Heo, C Seok - Nucleic acids research, 2019 - academic.oup.com
The 3D structure of a protein can be predicted from its amino acid sequence with high
accuracy for a large fraction of cases because of the availability of large quantities of …

High‐accuracy protein structures by combining machine‐learning with physics‐based refinement

L Heo, M Feig - Proteins: Structure, Function, and Bioinformatics, 2020 - Wiley Online Library
Protein structure prediction has long been available as an alternative to experimental
structure determination, especially via homology modeling based on templates from related …

GalaxyRefine: Protein structure refinement driven by side-chain repacking

L Heo, H Park, C Seok - Nucleic acids research, 2013 - academic.oup.com
The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …

GalaxyWEB server for protein structure prediction and refinement

J Ko, H Park, L Heo, C Seok - Nucleic acids research, 2012 - academic.oup.com
Three-dimensional protein structures provide invaluable information for understanding and
regulating biological functions of proteins. The GalaxyWEB server predicts protein structure …

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

A Kryshtafovych, T Schwede, M Topf… - Proteins: Structure …, 2019 - Wiley Online Library
CASP (critical assessment of structure prediction) assesses the state of the art in modeling
protein structure from amino acid sequence. The most recent experiment (CASP13 held in …

Critical assessment of methods of protein structure prediction (CASP)—Round XIV

A Kryshtafovych, T Schwede, M Topf… - Proteins: Structure …, 2021 - Wiley Online Library
Critical assessment of structure prediction (CASP) is a community experiment to advance
methods of computing three‐dimensional protein structure from amino acid sequence. Core …

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 …

2 : protein structure prediction server

CC Chen, JK Hwang, JM Yang - Nucleic acids research, 2006 - academic.oup.com
Protein structure prediction provides valuable insights into function, and comparative
modeling is one of the most reliable methods to predict 3D structures directly from amino …

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

J Moult, K Fidelis, A Kryshtafovych… - Proteins: Structure …, 2016 - Wiley Online Library
Modeling of protein structure from amino acid sequence now plays a major role in structural
biology. Here we report new developments and progress from the CASP11 community …

[HTML][HTML] The trRosetta server for fast and accurate protein structure prediction

Z Du, H Su, W Wang, L Ye, H Wei, Z Peng… - Nature protocols, 2021 - nature.com
The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …