I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction

DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning

(2022) Sai-Sai Guo et al.   BIOINFORMATICS

Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome

(2021) Chengxin Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Improved protein structure refinement guided by deep learning based accuracy estimation

(2021) Naozumi Hiranuma et al.   Nature Communications

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

Deep learning techniques have significantly impacted protein structure prediction and protein design

(2021) Robin Pearce et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Toward the solution of the protein structure prediction problem

(2021) Robin Pearce et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information

(2021) Shuwei Yao et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

(2021) Yang Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical Assessment of Methods of Protein Structure Prediction ( CASP ) – Round XIV

(2021) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions

(2021) S. M. Mortuza et al.   Nature Communications

Structure-based protein function prediction using graph convolutional networks

(2021) Vladimir Gligorijević et al.   Nature Communications

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

(2021) Alexandra Born et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The trRosetta server for fast and accurate protein structure prediction

(2021) Zongyang Du et al.   Nature Protocols

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior 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

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

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Grammar of protein domain architectures

(2019) Lijia Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Yang Li et al.   BIOINFORMATICS

INGA 2.0: improving protein function prediction for the dark proteome

(2019) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

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

Distance-based protein folding powered by deep learning

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

Evaluation of template‐based modeling in CASP13

(2019) Tristan I. Croll 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

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

(2019) Wei Zheng et al.   Future Generation Computer Systems-The International Journal of eScience

Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018–2019 Additions to neXtProt and the CAFA3 Challenge

(2019) Chengxin Zhang et al.   JOURNAL OF PROTEOME RESEARCH

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Activity and Affinity of Pin1 Variants

(2019) Alexandra Born et al.   MOLECULES

The cyanobacterial protoporphyrinogen oxidase HemJ is a newb-type heme protein functionally coupled with coproporphyrinogen III oxidase

(2018) Petra Skotnicová et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

(2018) Chengxin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Differential Evolution With Underestimation-Based Multimutation Strategy

(2018) Xiao-Gen Zhou et al.   IEEE Transactions on Cybernetics

Structure and Protein Interaction-based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17

(2018) Chengxin Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Towards region-specific propagation of protein functions

(2018) Da Chen Emily Koo et al.   BIOINFORMATICS

ConDo: protein domain boundary prediction using coevolutionary information

(2018) Seung Hwan Hong et al.   BIOINFORMATICS

C9orf72, a protein associated with amyotrophic lateral sclerosis (ALS) is a guanine nucleotide exchange factor

(2018) Shalini Iyer et al.   PeerJ

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database

(2017) John-Marc Chandonia et al.   JOURNAL OF MOLECULAR BIOLOGY

ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly

(2017) Yan Wang et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12

(2017) Chengxin Zhang 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

Abstract Convex Underestimation Assisted Multistage Differential Evolution

(2017) Xiao-Gen Zhou et al.   IEEE Transactions on Cybernetics

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

How good can cryo-EM become?

(2016) Robert M Glaeser   NATURE METHODS

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

(2015) Dong Xu et al.   BIOINFORMATICS

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

(2015) Frank DiMaio et al.   NATURE METHODS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Gene3D: expanding the utility of domain assignments

(2015) Su Datt Lam et al.   NUCLEIC ACIDS RESEARCH

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11

(2015) Wenxuan Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

(2014) Magnus Ekeberg et al.   JOURNAL OF COMPUTATIONAL PHYSICS

ThreaDom: extracting protein domain boundary information from multiple threading alignments

(2013) Zhidong Xue et al.   BIOINFORMATICS

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

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

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

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

DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning

(2011) Jesse Eickholt et al.   BMC BIOINFORMATICS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

(2011) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2011) Jian Zhang et al.   STRUCTURE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

(2009) Anna Lobley et al.   BIOINFORMATICS

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA