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A Pareto-Optimal Refinement Method for Protein Design Scaffolds
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Structure‐guided forcefield optimization
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De Novo Enzyme Design Using Rosetta3
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inferred← citeshttps://doi.org/10.1038/s41467-023-39890-8openalex-snapshot
Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants
inferred← citeshttps://doi.org/10.1038/s41467-023-40045-yopenalex-snapshot
GPCRome-wide analysis of G-protein-coupling diversity using a computational biology approach
inferred← citeshttps://doi.org/10.1038/s41467-023-41981-5openalex-snapshot
MYH10 activation rescues contractile defects in arrhythmogenic cardiomyopathy (ACM)
inferred← citeshttps://doi.org/10.1038/s41467-023-42163-zopenalex-snapshot
HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes
inferred← citeshttps://doi.org/10.1038/s41467-023-42255-wopenalex-snapshot
Phosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization
inferred← citeshttps://doi.org/10.1038/s41467-024-52582-1openalex-snapshot
De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants
inferred← citeshttps://doi.org/10.1038/s41467-025-58746-xopenalex-snapshot
Allosteric targeted drug delivery for enhanced blood-brain barrier penetration via mimicking transmembrane domain interactions
inferred← citeshttps://doi.org/10.1038/s41467-025-64365-3openalex-snapshot
Large protein-like leader peptides engage differently with RiPP halogenases and lanthionine synthetases
inferred← citeshttps://doi.org/10.1038/s41467-025-65311-zopenalex-snapshot
Protein-nucleic acid language model-assisted design of precise and compact adenine base editor
inferred← citeshttps://doi.org/10.1038/s41545-022-00170-5openalex-snapshot
Effective pathogen removal in sustainable natural fiber Moringa filters
inferred← citeshttps://doi.org/10.1038/s41551-025-01470-0openalex-snapshot
Directed evolution-based discovery of ligands for in vivo restimulation of chimeric antigen receptor T cells
inferred← citeshttps://doi.org/10.1038/s41556-022-01034-3openalex-snapshot
Caveolin-1 dolines form a distinct and rapid caveolae-independent mechanoadaptation system
inferred← citeshttps://doi.org/10.1038/s41564-022-01205-wopenalex-snapshot
Uropathogenic Escherichia coli subverts mitochondrial metabolism to enable intracellular bacterial pathogenesis in urinary tract infection
inferred← citeshttps://doi.org/10.1038/s41586-023-06068-7openalex-snapshot
γ-Linolenic acid in maternal milk drives cardiac metabolic maturation
inferred← citeshttps://doi.org/10.1038/s41586-023-06856-1openalex-snapshot
The PfRCR complex bridges malaria parasite and erythrocyte during invasion
inferred← citeshttps://doi.org/10.1038/s41587-024-02214-2openalex-snapshot
Computational scoring and experimental evaluation of enzymes generated by neural networks
inferred← citeshttps://doi.org/10.1038/s41589-022-01240-yopenalex-snapshot
SIRT1 deacetylates WEE1 and sensitizes cancer cells to WEE1 inhibition
inferred← citeshttps://doi.org/10.1038/s41594-019-0292-0openalex-snapshot
Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly
inferred← citeshttps://doi.org/10.1038/s41594-021-00636-zopenalex-snapshot
Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12
inferred← citeshttps://doi.org/10.1038/s41598-018-27118-5openalex-snapshot
Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine
inferred← citeshttps://doi.org/10.1038/s41598-019-43004-0openalex-snapshot
Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site
inferred← citeshttps://doi.org/10.1038/s41598-019-55266-9openalex-snapshot
Structural studies of the MMP-3 interaction with triple-helical collagen introduce new roles for the enzyme in tissue remodelling
inferred← citeshttps://doi.org/10.1038/s41598-021-84329-zopenalex-snapshot
Exploring targeting peptide-shell interactions in encapsulin nanocompartments
inferred← citeshttps://doi.org/10.1038/s41598-021-98977-8openalex-snapshot
Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies
inferred← citeshttps://doi.org/10.1038/s41598-022-07620-7openalex-snapshot
A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa
inferred← citeshttps://doi.org/10.1038/s41598-022-09133-9openalex-snapshot
Enoxaparin augments alpha-1-antitrypsin inhibition of TMPRSS2, a promising drug combination against COVID-19
inferred← citeshttps://doi.org/10.1038/s42003-022-03886-9openalex-snapshot
Coiled-coil structure of meiosis protein TEX12 and conformational regulation by its C-terminal tip
inferred← citeshttps://doi.org/10.1038/s44318-023-00026-9openalex-snapshot
MinD-RNase E interplay controls localization of polar mRNAs in E. coli
inferred← citeshttps://doi.org/10.1039/bk9781837670154-00327openalex-snapshot
Unsupervised Refinement of Protein Structures
inferred← citeshttps://doi.org/10.1039/c5tc03931bopenalex-snapshot
Docking-guided identification of protein hosts for GFP chromophore-like ligands
inferred← citeshttps://doi.org/10.1039/c8me00080hopenalex-snapshot
Role of antibody heavy and light chain interface residues in affinity maturation of binding to HIV envelope glycoprotein
inferred← citeshttps://doi.org/10.1039/d0cc01959copenalex-snapshot
Rosetta custom score functions accurately predict ΔΔ G of mutations at protein–protein interfaces using machine learning
inferred← citeshttps://doi.org/10.1039/d2me00153eopenalex-snapshot
Tuning a coiled-coil hydrogel via computational design of supramolecular fiber assembly
inferred← citeshttps://doi.org/10.1039/d3gc04888hopenalex-snapshot
Computational design of an efficient and thermostable esterase for polylactic acid depolymerization
inferred← citeshttps://doi.org/10.1039/d4bm00354copenalex-snapshot
Engineered coiled-coil HIF1α protein domain mimic
inferred← citeshttps://doi.org/10.1042/bcj20230067openalex-snapshot
Dimerization and autophosphorylation of the MST family of kinases are controlled by the same set of residues
inferred← citeshttps://doi.org/10.1042/bcj20230139openalex-snapshot
Computational design of Matrix Metalloproteinase-9 (MMP-9) resistant to auto-cleavage
inferred← citeshttps://doi.org/10.1073/pnas.1908723117openalex-snapshot
A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures
inferred← citeshttps://doi.org/10.1073/pnas.2011448117openalex-snapshot
DNA binding induces a cis -to- trans switch in Cre recombinase to enable intasome assembly
inferred← citeshttps://doi.org/10.1073/pnas.2104242118openalex-snapshot
A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization
inferred← citeshttps://doi.org/10.1073/pnas.2305494120openalex-snapshot
Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold
inferred← citeshttps://doi.org/10.1073/pnas.2311500121openalex-snapshot
An all-atom protein generative model
inferred← citeshttps://doi.org/10.1073/pnas.2414756122openalex-snapshot
Symmetry facilitated the evolution of heterospecificity and high-order stoichiometry in vertebrate hemoglobin
inferred← citeshttps://doi.org/10.1073/pnas.2512358122openalex-snapshot
Machine learning enables de novo multiepitope design of Plasmodium falciparum circumsporozoite protein to target trimeric L9 antibody
inferred← citeshttps://doi.org/10.1074/jbc.ra117.001289openalex-snapshot
Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh in
inferred← citeshttps://doi.org/10.1074/jbc.ra118.006113openalex-snapshot
Unraveling the structural elements of pH sensitivity and substrate binding in the human zinc transporter SLC39A2 (ZIP2)
inferred← citeshttps://doi.org/10.1074/jbc.ra119.008404openalex-snapshot
A molecular model for self-assembly of the synaptonemal complex protein SYCE3
inferred← citeshttps://doi.org/10.1074/jbc.ra120.014889openalex-snapshot
A clinically relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position
inferred← citeshttps://doi.org/10.1080/07391102.2023.2252901openalex-snapshot
In silico and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis
inferred← citeshttps://doi.org/10.1080/07391102.2024.2329785openalex-snapshot
Enhancing bezlotoxumab binding to C. difficile toxin B2: insights from computational simulations and mutational analyses for antibody design
inferred← citeshttps://doi.org/10.1080/14756366.2018.1491564openalex-snapshot
Donepezil structure-based hybrids as potential multifunctional anti-Alzheimer’s drug candidates
inferred← citeshttps://doi.org/10.1080/14756366.2019.1677638openalex-snapshot
A structure-based approach towards the identification of novel antichagasic compounds: Trypanosoma cruzi carbonic anhydrase inhibitors
inferred← citeshttps://doi.org/10.1080/15548627.2023.2284523openalex-snapshot
Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles
inferred← citeshttps://doi.org/10.1083/jcb.202002077openalex-snapshot
Mutual antagonism between Hippo signaling and cyclin E drives intracellular pattern formation
inferred← citeshttps://doi.org/10.1088/1361-6633/ac78efopenalex-snapshot
Key aspects of the past 30 years of protein design
inferred← citeshttps://doi.org/10.1089/cmb.2024.0866openalex-snapshot
VIPER: Virus Inhibition Via Peptide Engineering and Receptor Mimicry
inferred← citeshttps://doi.org/10.1093/bib/bbaf477openalex-snapshot
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa1050openalex-snapshot
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty975openalex-snapshot
A structural homology approach for computational protein design with flexible backbone
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz657openalex-snapshot
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes
inferred← citeshttps://doi.org/10.1093/braincomms/fcac243openalex-snapshot
Differential regulation of insulin signalling by monomeric and oligomeric amyloid beta-peptide
inferred← citeshttps://doi.org/10.1093/hmg/ddz081openalex-snapshot
Pathogenic effects of agrin V1727F mutation are isoform specific and decrease its expression and affinity for HSPGs and LRP4
inferred← citeshttps://doi.org/10.1093/protein/gzad012openalex-snapshot
Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs
inferred← citeshttps://doi.org/10.1093/protein/gzu005openalex-snapshot
An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network
inferred← citeshttps://doi.org/10.1093/protein/gzz007openalex-snapshot
Computational-guided determination of the functional role of 447-52D long CDRH3
inferred← citeshttps://doi.org/10.1096/fj.202001808ropenalex-snapshot
Predicting susceptibility to SARS‐CoV‐2 infection based on structural differences in ACE2 across species
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