Citation Impact
Citing Papers
Coevolutionary signals across protein lineages help capture multiple protein conformations
2013
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
The Protein-Folding Problem, 50 Years On
2012 Science
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
2021
Origins of coevolution between residues distant in protein 3D structures
2017 StandoutNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences
2015
Inferring interaction partners from protein sequences
2016
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
From residue coevolution to protein conformational ensembles and functional dynamics
2015
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
2013 StandoutNobel
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis
2012
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
2012
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN
2024 StandoutNobel
Generative models for graph-based protein design
2019
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI
2016
Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
2019
Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age
2017
Hierarchical design of pseudosymmetric protein nanocages
2024 StandoutNatureNobel
The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach
2021 StandoutNobel
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4
2015 StandoutNobel
Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
2022 StandoutNobel
FreeContact: fast and free software for protein contact prediction from residue co-evolution
2014
Predicting multiple conformations via sequence clustering and AlphaFold2
2023 Nature
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
2022 StandoutNobel
Machine learning for functional protein design
2024
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
2017
Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions
2024 StandoutNobel
Multistate and functional protein design using RoseTTAFold sequence space diffusion
2024 StandoutNobel
Inferring interaction partners from protein sequences using mutual information
2018
Structure of the Type VI Secretion System Contractile Sheath
2015 StandoutNobel
Deep generative models of genetic variation capture the effects of mutations
2018
Protein structure prediction from sequence variation
2012
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
2016 Standout
Machine learning in protein structure prediction
2021
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
2014
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3
2017 StandoutNatureNobel
Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis
2018 StandoutNobel
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
2013
Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates
2019 Standout
Advances in protein structure prediction and design
2019
Capturing coevolutionary signals inrepeat proteins
2015
Improved protein structure refinement guided by deep learning based accuracy estimation
2021 StandoutNobel
Causes of evolutionary rate variation among protein sites
2016
High-performance medicine: the convergence of human and artificial intelligence
2018 Standout
The coming of age of de novo protein design
2016 StandoutNatureNobel
Ultra-large alignments using phylogeny-aware profiles
2015
Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks
2017
A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain
2019 StandoutNobel
The Transporter Classification Database (TCDB): recent advances
2015
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
Structured States of Disordered Proteins from Genomic Sequences
2016
The computational prediction of protein assemblies
2017
Exploring protein-protein interactions at the proteome level
2022
Mutation effects predicted from sequence co-variation
2017
The ChEMBL database in 2017
2016 Standout
Predicting functional effect of missense variants using graph attention neural networks
2022
Dimeric interactions and complex formation using direct coevolutionary couplings
2015
Emerging methods in protein co-evolution
2013
Protein 3D Structure Computed from Evolutionary Sequence Variation
2011
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
2016
Protein structure determination by combining sparse NMR data with evolutionary couplings
2015
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
2012
A General Computational Approach for Repeat Protein Design
2014 StandoutNobel
De novo protein design by deep network hallucination
2021 StandoutNatureNobel
Large language models generate functional protein sequences across diverse families
2023
Improving Protein Expression, Stability, and Function with ProteinMPNN
2024 StandoutNobel
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
2018
Epistasis in protein evolution
2016
Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis
2015
Transplantation of prokaryotic two-component signaling pathways into mammalian cells
2014
SWISS-MODEL: homology modelling of protein structures and complexes
2018 Standout
One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling
2013 StandoutNobel
An evolution-based model for designing chorismate mutase enzymes
2020 Science
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers
2017
R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter
2016
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
2019 StandoutNobel
ComplexContact: a web server for inter-protein contact prediction using deep learning
2018
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
2014 StandoutNobel
Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 StandoutScience
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
Limits in accuracy and a strategy of RNA structure prediction using experimental information
2019
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks
2019
Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation
2014
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks
2018
Structural insight into TRPV5 channel function and modulation
2019 StandoutNobel
Large-scale determination of previously unsolved protein structures using evolutionary information
2015 StandoutNobel
A deep learning framework for improving long-range residue–residue contact prediction using a hierarchical strategy
2017
Sequence co-evolution gives 3D contacts and structures of protein complexes
2014
Genomics-aided structure prediction
2012
Accurate proteome-wide missense variant effect prediction with AlphaMissense
2023 StandoutScienceNobel
Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1
2014
Comparative sequence analysis suggests a conserved gating mechanism for TRP channels
2015
Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials
2016 Standout
Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13
2019
Protein contact prediction using metagenome sequence data and residual neural networks
2019 StandoutNobel
Works of Bryan Lunt being referenced
Inference of Direct Residue Contacts in Two-Component Signaling
2010
Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks
2011
Major Facilitator Superfamily Porters, LacY, FucP and XylE of Escherichia coli Appear to Have Evolved Positionally Dissimilar Catalytic Residues without Rearrangement of 3-TMS Repeat Units
2014
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
2011
Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families
2012