Protein Science

Article	Citations
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions	969
PANTHER: Making genome‐scale phylogenetics accessible to all	815
UCSF ChimeraX: Tools for structure building and analysis	575
KEGG mapping tools for uncovering hidden features in biological data	427
DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data	258
DALI shines a light on remote homologs: One hundred discoveries	215
BenchmarkingAlphaFoldfor protein complex modeling reveals accuracy determinants	192
Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences	141
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0	136
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	134
The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis	133
Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins	124
The Human Protein Atlas—Spatial localization of the human proteome in health and disease	121
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	103
Leginon: New features and applications	102
Nanodiscs: A toolkit for membrane protein science	93
AlphaFold2 fails to predict protein fold switching	90
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	85
PANNZER—A practical tool for protein function prediction	77
DIALS as a toolkit	75
BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models	75
Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	72
Interplay between tau and α‐synuclein liquid–liquid phase separation	63
Intrinsic protein disorder and conditional folding in AlphaFoldDB	59
Structural and functional understanding of the toll‐like receptors	56

Multiple sites on SARS‐CoV‐2 spike protein are susceptible to proteolysis by cathepsins B, K, L, S, and V	53
PDB‐101: Educational resources supporting molecular explorations through biology and medicine	52
Rapid prediction and analysis of protein intrinsic disorder	50
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	50
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	48
Evaluation of AlphaFold2 structures as docking targets	45
In‐depth interrogation of protein thermal unfolding data with MoltenProt	45
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D	44
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps	44
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8	43
Liquid–liquid phase separation of Tau by self and complex coacervation	42
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	42
NMR hawk‐eyed view of AlphaFold2 structures	42
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	41
Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure	39
Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations	35
CMM—An enhanced platform for interactive validation of metal binding sites	35
Crosslinking mass spectrometry: A link between structural biology and systems biology	34
De novo protein design by inversion of the AlphaFold structure prediction network	33
N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma	32
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data	32
Unveiling the binding mode of perfluorooctanoic acid to human serum albumin	30
Templates for writing PyMOL scripts	30
Structural basis for the interaction of SARS‐CoV‐2 virulence factor nsp1 with DNA polymerase α–primase	28
FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains	27
AMP‐BERT: Prediction of antimicrobial peptide function based on a BERT model	27
Electrostatic modulation of hnRNPA1 low‐complexity domain liquid–liquid phase separation and aggregation	26
The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes	26
Mechanisms of protein evolution	25
Resolving the enthalpy of protein stabilization by macromolecular crowding	25
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	25
Protein folding ‐ seeing is deceiving	25
Crystal structure of SARS‐CoV‐2 nsp10–nsp16 in complex with small molecule inhibitors, SS148 and WZ16	25
Measuring gas vesicle dimensions by electron microscopy	25
AlphaFold predicts the most complex protein knot and composite protein knots	25
Initiation of focal adhesion assembly by talin and kindlin: A dynamic view	24
Thioesterase enzyme families: Functions, structures, and mechanisms	24
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	24
Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation	23
Prokaryote toxin–antitoxin modules: Complex regulation of an unclear function	23
DNA‐binding domain as the minimal region driving RNA‐dependent liquid–liquid phase separation of androgen receptor	23
ATP regulates RNA‐driven cold inducible RNA binding protein phase separation	23
BayeStab: Predicting effects of mutations on protein stability with uncertainty quantification	23
CTD of SARS‐CoV‐2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation	23
Evaluation ofAlphaFoldantibody–antigen modeling with implications for improving predictive accuracy	23
Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models	22
Cryptochromes: Photochemical and structural insight into magnetoreception	22
AlphaFold predicts novel human proteins with knots	22
DPAM: A domain parser for AlphaFold models	22
A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer	21

The regulation of DNA supercoiling across evolution	20
Vitamin D and COVID‐19: A review on the role of vitamin D in preventing and reducing the severity of COVID‐19 infection	20
Small heat shock protein 22 kDa can modulate the aggregation and liquid–liquid phase separation behavior of tau	20
Arginine multivalency stabilizes protein/RNA condensates	19
Consensus mutagenesis approach improves the thermal stability of system xc− transporter, xCT, and enables cryo‐EM analyses	19
New covalent bonding ability for proteins	19
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	19
Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase	19
Nonstructural protein 7 and 8 complexes of SARS‐CoV‐2	18
Computational design of mixed chirality peptide macrocycles with internal symmetry	18
Cyclic nucleotide selectivity of protein kinase G isozymes	18
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	18
Molecular insights into the primary nucleation of polymorphic amyloid β dimers in DOPC lipid bilayer membrane	17
A systematic analysis of the beta hairpin motif in the Protein Data Bank	17
Protection by desiccation‐tolerance proteins probed at the residue level	17
X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology	17
The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove	16
KEGG tools for classification and analysis of viral proteins	16
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library	16
Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay	16
Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain	16
The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases	16
Local sequence‐structure relationships in proteins	16
CHARMM‐GUIhigh‐throughput simulator for efficient evaluation of protein–ligand interactions with different force fields	15
A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices	15
HDOCK update for modeling protein‐RNA/DNA complex structures	15
Nicking and fragmentation are responsible for α‐lactalbumin amyloid fibril formation at acidic pH and elevated temperature	15
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	15
Flash properties of Gaussia luciferase are the result of covalent inhibition after a limited number of cycles	15
The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX‐MS, DSC, and nanoDSF	15
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	15
Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana	15
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	15
Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans	15
Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin	14
CyDisCo production of functional recombinant SARS‐CoV‐2 spike receptor binding domain	14
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	14
Python‐based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier–Bessel indexing of electron microscopic data	14
Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation	14
Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint	14
Frontotemporal dementia‐linked P112H mutation of TDP‐43 induces protein structural change and impairs its RNA binding function	14
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	14
Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	14
Assessing and enhancing foldability in designed proteins	13
Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase	13
Allostery‐driven changes in dynamics regulate the activation of bacterial copper transcription factor	13
Similar protein segments shared between domains of different evolutionary lineages	13
Computed cancer interactome explains the effects of somatic mutations in cancers	13
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	13
Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates	13
Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein	13
Simple mechanisms for the evolution of protein complexity	13
The human protein atlas—Integrated omics for single cell mapping of the human proteome	13
Complementing machine learning‐based structure predictions with native mass spectrometry	13
Three‐repeat and four‐repeat tau isoforms form different oligomers	13
PDBsum1: A standalone program for generating PDBsum analyses	13
The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA‐binding proteins for liquid–liquid phase separation	13
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	12
An apparent core/shell architecture of polyQ aggregates in the aging Caenorhabditis elegans neuron	12
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry	12
Stability profile of vimentin rod domain	12
Differences in the dynamics of the tandem‐SH2 modules of the Syk and ZAP‐70 tyrosine kinases	12
Functional analysis of protein post‐translational modifications using genetic codon expansion	12
In vivo liquid–liquid phase separation protects amyloidogenic and aggregation‐prone peptides during overexpression in Escherichia coli	12
Estimating conformational heterogeneity of tryptophan synthase with a template‐based Alphafold2 approach	12
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	12
Distinguishing features of fold‐switching proteins	12
Genetically encoded crosslinkers to address protein–protein interactions	12
Time Resolved‐Fluorescence Resonance Energy Transfer platform for quantitative nucleosome binding and footprinting	11
Learning deep representations of enzyme thermal adaptation	11
Water‐mediated interactions destabilize proteins	11
The antimicrobial peptide database is 20 years old: Recent developments and future directions	11
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	11
The roles of highly conserved, non‐catalytic residues in class A β‐lactamases	11
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern	11
High‐efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices	11
Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme	11
Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family	11
A new kid in the folding funnel: Molecular chaperone activities of the BRICHOS domain	11
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins	11

Intrinsic protein disorder uncouples affinity from binding specificity	11
Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid	11
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	11
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods	10
Phenotypic mutations contribute to protein diversity and shape protein evolution	10
QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets	10
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning	10
A genetically encoded far‐red fluorescent calcium ion biosensor derived from a biliverdin‐binding protein	10
Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins	10
Heterologous expression of naturally evolved putative de novo proteins with chaperones	10
Ca2+‐dependent interactions between lipids and the tumor‐targeting peptide pHLIP	10
Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors	10
Biomolecular phase separation through the lens of sodium‐23 NMR	10
Extension of a de novo TIM barrel with a rationally designed secondary structure element	10
Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes	10
Development of in vivo HDX‐MS with applications to a TonB‐dependent transporter and other proteins	10
Compendium of causative genes and their encoded proteins for common monogenic disorders	10
Molecular insights into α‐synuclein interaction with individual human core histones, linker histone, and dsDNA	10
3,4‐Dihydroxyphenylethanol and 3,4‐dihydroxyphenylacetic acid affect the aggregation process of E46K variant of α‐synuclein at different extent: Insights into the interplay between protein	10
Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes	10
How enzymes harness highly unfavorable proton transfer reactions	10
Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold	10
Discovery of antimicrobial agent targeting tryptophan synthase	10
Predictable fold switching by theSARS‐CoV‐2 proteinORF9b	10
A newly introduced salt bridge cluster improves structural and biophysical properties of de novoTIM barrels	10
Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor	10
A hierarchical deep learning based approach for multi‐functional enzyme classification	9
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	9
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation	9
Pyrexia and acidosis act independently of neutrophil elastase reactive center loop cleavage to effect cortisol release from corticosteroid‐binding globulin	9
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	9
Structural basis for substrate specificity of l‐methionine decarboxylase	9
Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane	9
Dockground resource for protein recognition studies	9
Design and optimization of enzymatic activity in a de novo β‐barrel scaffold	9
Thermodynamic coupling between neighboring binding sites in homo‐oligomeric ligand sensing proteins from mass resolved ligand‐dependent population distributions	9
Capturing the geometry, function, and evolution of enzymes with 3D templates	9
Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors	9
Dissecting the structural heterogeneity of proteins by native mass spectrometry	9
Structural motifs in protein cores and at protein–protein interfaces are different	9
IEDB‐3D 2.0: Structural data analysis within the Immune Epitope Database	9
L‐serine biosynthesis in the human central nervous system: Structure and function of phosphoserine aminotransferase	9
Structure of the human Ccr4‐Not nuclease module using X‐ray crystallography and electron paramagnetic resonance spectroscopy distance measurements	9
Correspondence between functional scores from deep mutational scans and predicted effects on protein stability	9
Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation	9
Design of a H2O2‐generating P450SPα fusion protein for high yield fatty acid conversion	9
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	9
Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry	9
The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z	9
Protein yoga: Conformational versatility of the Hemolysin II C‐terminal domain detailed by NMR structures for multiple states	9
Topiary: Pruning the manual labor from ancestral sequence reconstruction	9
Expanding the genetic code	9
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates	9
Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3	9
Zero‐shot mutation effect prediction on protein stability and function using RoseTTAFold	9
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	9
Characterization of the Escherichia coli pyridoxal 5′‐phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability	9
Cardiolipin interacts with beta‐2‐glycoprotein I and forms an open conformation–Mechanisms analyzed using hydrogen/deuterium exchange	8
DbStRiPs: Database of structural repeats in proteins	8
Insect cell expression and purification of recombinant SARS‐COV‐2 spike proteins that demonstrate ACE2 binding	8
Revisiting the phosphotyrosine binding pocket of Fyn SH2 domain led to the identification of novel SH2 superbinders.	8
A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP‐43 and modulates its phase behavior	8
Structural insights into the tropomodulin assembly at the pointed ends of actin filaments	8
Tertiary motifs as building blocks for the design of protein‐binding peptides	8
The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function	8
The MECP2‐TRD domain interacts with the DNMT3A‐ADD domain at the H3‐tail binding site	8
Stabilizing proteins, simplified: A Rosetta‐based webtool for predicting favorable mutations	8
Trifluoroethanol and the behavior of a tardigrade desiccation‐tolerance protein	8
Pulse‐field gradient nuclear magnetic resonance of protein translational diffusion from native to non‐native states	8
Substitutions at a rheostat position in human aldolase A cause a shift in the conformational population	8
Aromaticity at position 39 in α‐synuclein: A modulator of amyloid fibril assembly and membrane‐bound conformations	8
Hydrophobicity‐enhanced ferritin nanoparticles for efficient encapsulation and targeted delivery of hydrophobic drugs to tumor cells	8
LambdaPP: Fast and accessible protein‐specific phenotype predictions	8
SSDraw: Software for generating comparative protein secondary structure diagrams	8
Uniform binding and negative catalysis at the origin of enzymes	8
“Not‐so‐popular” orthogonal pairs in genetic code expansion	8
Structural dynamics of the complex of calmodulin with a minimal functional construct of eukaryotic elongation factor 2 kinase and the role of Thr348 autophosphorylation	8
Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices	8
Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif	8
Optimal structure determination from sub‐optimal diffraction data	8
NKp46‐specific single domain antibodies enable facile engineering of various potent NK cell engager formats	8
Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations	8
Structure‐based design of a photoswitchable affibody scaffold	8
Innovation and tinkering in the evolution of oxidases	8
Recognizing lysine–cysteine crosslinks in proteins	7
Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation	7
Shape shifting: The multiple conformational substates of the PTEN N‐terminal PIP2‐binding domain	7
Epitope mapping of novel monoclonal antibodies to human angiotensin I‐converting enzyme	7
Higher‐order interactions of Bcr‐Abl can broaden chronic myeloid leukemia (CML) drug repertoire	7
Activity and substrate specificity of lytic polysaccharide monooxygenases: An ATR FTIR‐based sensitive assay tested on a novel species from Pseudomonas putida	7
Structural and functional study of Legionella pneumophila effector RavA	7
ATP‐independent molecular chaperone activity generated under reducing conditions	7
DomainMapper: Accurate domain structure annotation including those with non‐contiguous topologies	7
Depicting the proton relay network in human aromatase: New insights into the role of the alcohol‐acid pair	7
High‐throughput cell‐free screening of eukaryotic membrane protein expression in lipidic mimetics	7