Improved protein structure prediction using predicted interresidue orientations

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

(2019) Yang Li et al.   BIOINFORMATICS

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

(2019) Jie Hou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein contact prediction using metagenome sequence data and residual neural networks

(2019) Qi Wu et al.   BIOINFORMATICS

De novo protein design by citizen scientists

(2019) Brian Koepnick et al.   NATURE

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

(2019) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of model refinement in CASP13

(2019) Randy J. Read et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

(2019) Shaun M. Kandathil et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Driven to Near‐Experimental Accuracy by Refinement via Molecular Dynamics Simulations

(2019) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High‐accuracy refinement using Rosetta in CASP13

(2019) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

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

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

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

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

(2017) Sheng Wang et al.   PLoS Computational Biology

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

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