Standout Papers
Citation Impact
Citing Papers
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN
2024 StandoutNobel
Sculpting conducting nanopore size and shape through de novo protein design
2024 StandoutScienceNobel
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
2023
Protein oligomer modeling guided by predicted interchain contacts in CASP14
2021 StandoutNobel
Assessing the utility of CASP14 models for molecular replacement
2021
High‐accuracy refinement using Rosetta in CASP13
2019 StandoutNobel
Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function
2024 StandoutNobel
Hierarchical design of pseudosymmetric protein nanocages
2024 StandoutNatureNobel
Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists
2024 StandoutScienceNobel
Expansive discovery of chemically diverse structured macrocyclic oligoamides
2024 StandoutScienceNobel
Design of a mucin-selective protease for targeted degradation of cancer-associated mucins
2023 Nobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
A suite of designed protein cages using machine learning and protein fragment-based protocols
2024
De novo design of allosterically switchable protein assemblies
2024 StandoutNatureNobel
General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept
2018
Predicting multiple conformations via sequence clustering and AlphaFold2
2023 Nature
Sampling of structure and sequence space of small protein folds
2022 StandoutNobel
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
2022 StandoutNobel
2023 Standout
Multistate and functional protein design using RoseTTAFold sequence space diffusion
2024 StandoutNobel
PLIP: fully automated protein–ligand interaction profiler
2015 Standout
The ClusPro web server for protein–protein docking
2017 Standout
Improving de novo protein binder design with deep learning
2023 StandoutNobel
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
De novo design of luciferases using deep learning
2023 StandoutNatureNobel
Large language models in medicine
2023 Standout
The trRosetta server for fast and accurate protein structure prediction
2021 StandoutNobel
Advances in protein structure prediction and design
2019
Improved protein structure refinement guided by deep learning based accuracy estimation
2021 StandoutNobel
What method to use for protein–protein docking?
2019
The Origin of Consistent Protein Structure Refinement from Structural Averaging
2015 StandoutNobel
Leveraging crosslinking mass spectrometry in structural and cell biology
2021
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System
2015
Rational design of photosynthetic reaction center protein maquettes
2022
The Biology of CRISPR-Cas: Backward and Forward
2018 StandoutNobel
Programmable protein delivery with a bacterial contractile injection system
2023 Nature
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA
2023 StandoutNobel
The HDOCK server for integrated protein–protein docking
2020
De novo protein design by deep network hallucination
2021 StandoutNatureNobel
Large language models generate functional protein sequences across diverse families
2023
Protein structure predictions to atomic accuracy with AlphaFold
2022 StandoutNobel
De novo protein design by inversion of the AlphaFold structure prediction network
2023
Improving Protein Expression, Stability, and Function with ProteinMPNN
2024 StandoutNobel
Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines
2013
Evaluation of predictions in the CASP10 model refinement category
2013
Lysosomal cathepsin D mediates endogenous mucin glycodomain catabolism in mammals
2022 StandoutNobel
2015 StandoutNobel
Critical assessment of methods of protein structure prediction (CASP)—Round XIII
2019
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks
2023 StandoutNobel
Automatic structure prediction of oligomeric assemblies using Robetta in CASP12
2017 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
Computational protein structure refinement: almost there, yet still so far to go
2017
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
The Protein Structure Prediction Revolution and Its Implications for Medicine
2023 StandoutNobel
Assessment of the model refinement category in CASP12
2017
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics
2016
Latest developments in molecular docking: 2010–2011 in review
2013
refineD: improved protein structure refinement using machine learning based restrained relaxation
2019
Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking
2019 StandoutNobel
Top-down design of protein architectures with reinforcement learning
2023 StandoutScienceNobel
Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site
2023 StandoutNobel
Accurate proteome-wide missense variant effect prediction with AlphaMissense
2023 StandoutScienceNobel
Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold
2022 Science
Works of Lim Heo being referenced
Experimental accuracy in protein structure refinement via molecular dynamics simulations
2018
What makes it difficult to refine protein models further via molecular dynamics simulations?
2017
ColabFold: making protein folding accessible to all
2022 Standout
GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking
2016
LigDockCSA: Protein–ligand docking using conformational space annealing
2011
Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments
2014
GalaxyWEB server for protein structure prediction and refinement
2012
GalaxyRefine: protein structure refinement driven by side-chain repacking
2013
GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
2015
GalaxySite: ligand-binding-site prediction by using molecular docking
2014
GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure
2017
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
2019
Driven to near‐experimental accuracy by refinement via molecular dynamics simulations
2019
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment
2017
Physics‐based protein structure refinement in the era of artificial intelligence
2021
Effective protein model structure refinement by loop modeling and overall relaxation
2015
Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment
2017