Toward the solution of the protein structure prediction problem

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

ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities

(2021) Jaie Woodard et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

(2020) Chengxin Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand–Receptor Interactions

(2020) Wallace K.B. Chan et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting the Real‐Valued Inter‐Residue Distances for Proteins

(2020) Wenze Ding et al.   Advanced Science

Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in silico Structure-Based Virtual Screening Approach

(2020) Shweta Choudhary et al.   Frontiers in Immunology

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

(2020) Ewen Callaway   NATURE

Discovery of ARD-69 as a Highly Potent Proteolysis Targeting Chimera (PROTAC) Degrader of Androgen Receptor (AR) for the Treatment of Prostate Cancer

(2019) Xin Han et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2019) Yang Li et al.   BIOINFORMATICS

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Protein contact prediction using metagenome sequence data and residual neural networks

(2019) Qi Wu et al.   BIOINFORMATICS

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

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

Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

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

Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell

(2019) Antonio Deiana et al.   PLoS One

Distance-based protein folding powered by deep learning

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

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

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

(2019) Joe G. Greener et al.   Nature Communications

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

(2019) Wei Zheng et al.   PLoS Computational Biology

Protein threading using residue co-variation and deep learning

(2018) Jianwei Zhu et al.   BIOINFORMATICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

(2018) Yang Liu et al.   Cell Systems

GenBank

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Experimental accuracy in protein structure refinement via molecular dynamics simulations

(2018) Lim Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Evaluation of the template-based modeling in CASP12

(2017) Andriy Kryshtafovych 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

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?

(2016) Jeffrey Skolnick et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

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

Mutation Drivers of Immunological Responses to Cancer

(2016) E. Porta-Pardo et al.   Cancer Immunology Research

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning

(2015) Jianzhu Ma et al.   BIOINFORMATICS

Single-Particle Cryo-EM at Crystallographic Resolution

(2015) Yifan Cheng   CELL

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

Improving accuracy of protein contact prediction using balanced network deconvolution

(2015) Hai-Ping Sun et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome

(2015) Jian Zhang et al.   STRUCTURE

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

Cancer3D: understanding cancer mutations through protein structures

(2014) Eduard Porta-Pardo et al.   NUCLEIC ACIDS RESEARCH

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

PconsC: combination of direct information methods and alignments improves contact prediction

(2013) Marcin J. Skwark et al.   BIOINFORMATICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

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

Toward optimal fragment generations forab initioprotein structure assembly

(2013) Dong Xu et al.   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

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

(2013) Dong Xu et al.   Scientific Reports

Unusual biophysics of intrinsically disordered proteins

(2012) Vladimir N. Uversky   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs

(2012) Hongyi Zhou et al.   MOLECULAR PHARMACEUTICS

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

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

Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement

(2012) Ambrish Roy et al.   STRUCTURE

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Michael Remmert et al.   NATURE METHODS

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

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

(2011) Jian Zhang et al.   STRUCTURE

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

(2010) Z. Wang et al.   BIOINFORMATICS

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

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

(2010) Ambrish Roy et al.   Nature Protocols

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns

(2009) Yan Yuan Tseng et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

NNcon: improved protein contact map prediction using 2D-recursive neural networks

(2009) A. N. Tegge et al.   NUCLEIC ACIDS RESEARCH

Prediction of membrane protein structures with complex topologies using limited constraints

(2009) P. Barth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

(2009) Ian Walsh et al.   BMC STRUCTURAL BIOLOGY

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

(2008) Sitao Wu et al.   BIOINFORMATICS

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction

(2008) Sitao Wu et al.   PLoS One

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

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

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

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting residue-residue contact maps by a two-layer, integrated neural-network method

(2008) Bin Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS