OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions

(2023) Nabin Giri et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling

(2023) Gang Xu et al.   Journal of Chemical Theory and Computation

Studying protein–protein interaction through side-chain modeling method OPUS-Mut

(2022) Gang Xu et al.   BRIEFINGS IN BIOINFORMATICS

OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding

(2021) Gang Xu et al.   BIOINFORMATICS

pyconsFold: a fast and easy tool for modeling and docking using distance predictions

(2021) J Lamb et al.   BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling

(2020) Gang Xu et al.   Journal of Chemical Theory and Computation

OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods

(2020) Gang Xu et al.   Journal of Chemical Information and Modeling

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

EvoEF2: accurate and fast energy function for computational protein design

(2019) Xiaoqiang Huang et al.   BIOINFORMATICS

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores

(2018) Grigore Pintilie et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2017) Jürgen Haas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

CONFOLD: Residue-residue contact-guidedab initioprotein folding

(2015) Badri Adhikari et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps

(2012) Steffen Lindert et al.   STRUCTURE

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE