Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

(2021) Yang Li et al.   PLoS Computational Biology

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

FASPR: an open-source tool for fast and accurate protein side-chain packing

(2020) Xiaoqiang Huang et al.   BIOINFORMATICS

FUpred: detecting protein domains through deep-learning-based contact map prediction

(2020) Wei Zheng et al.   BIOINFORMATICS

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

(2019) Yang Li et al.   BIOINFORMATICS

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

(2019) Wei Zheng et al.   NUCLEIC ACIDS RESEARCH

Assembling multidomain protein structures through analogous global structural alignments

(2019) Xiaogen Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13

(2019) Yang Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins

(2019) Chengxin Zhang et al.   BIOINFORMATICS

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

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Detecting distant-homology protein structures by aligning deep neural-network based contact maps

(2019) Wei Zheng et al.   PLoS Computational Biology

HMMER web server: 2018 update

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

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

ResQ: An Approach to Unified Estimation of B -Factor and Residue-Specific Error in Protein Structure Prediction

(2016) Jianyi Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

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

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

I-TASSER server: new development for protein structure and function predictions

(2015) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

(2015) Armin Meier et al.   PLoS Computational Biology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures

(2014) Jungkap Park et al.   BMC BIOINFORMATICS

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

(2014) Jianzhu Ma et al.   PLoS Computational Biology

ThreaDom: extracting protein domain boundary information from multiple threading alignments

(2013) Zhidong Xue et al.   BIOINFORMATICS

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

(2013) Dong Xu et al.   BIOINFORMATICS

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Toward optimal fragment generations forab initioprotein structure assembly

(2013) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

(2013) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

(2011) Dong Xu et al.   BIOPHYSICAL JOURNAL

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

(2011) Michael Remmert et al.   NATURE METHODS

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

(2008) Sitao Wu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS