Protein Science

Article	Citations
UCSF ChimeraX: Structure visualization for researchers, educators, and developers	4322
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions	730
PANTHER: Making genome‐scale phylogenetics accessible to all	454
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data	389
KEGG mapping tools for uncovering hidden features in biological data	344
Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2	265
DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations	231
DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data	200
Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein	193
The Bio3D packages for structural bioinformatics	190
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants	129
DALI shines a light on remote homologs: One hundred discoveries	97
The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis	95
The Human Protein Atlas—Spatial localization of the human proteome in health and disease	94
Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences	93
UCSF ChimeraX: Tools for structure building and analysis	91
Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins	84
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0	84
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	81
The AutoDock suite at 30	81
Nanodiscs: A toolkit for membrane protein science	74
Leginon: New features and applications	73
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	68
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	64
AlphaFold2 fails to predict protein fold switching	62

DIALS as a toolkit	53
Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	53
PANNZER—A practical tool for protein function prediction	51
PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system	50
Interplay between tau and α‐synuclein liquid–liquid phase separation	49
A mechanistic view of enzyme evolution	48
Comparing the binding properties of peptides mimicking the Envelope protein of SARS‐CoV and SARS‐CoV‐2 to the PDZ domain of the tight junction‐associated PALS1	47
Toward a new picture of the living plasma membrane	44
Progress toward Alzheimer's disease treatment: Leveraging the Achilles' heel of Aβ oligomers?	44
The function of histone lysine methylation related SET domain group proteins in plants	44
Multiple sites on SARS‐CoV‐2 spike protein are susceptible to proteolysis by cathepsins B, K, L, S, and V	44
Structural and functional understanding of the toll‐like receptors	43
How to use the MEROPS database and website to help understand peptidase specificity	43
PDB‐101: Educational resources supporting molecular explorations through biology and medicine	41
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8	40
Intrinsic protein disorder and conditional folding in AlphaFoldDB	40
NMR hawk‐eyed view of AlphaFold2 structures	38
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	37
BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models	34
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps	33
In‐depth interrogation of protein thermal unfolding data with MoltenProt	33
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	32
Rapid prediction and analysis of protein intrinsic disorder	32
Liquid–liquid phase separation of Tau by self and complex coacervation	32
Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure	29
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	29
Insulin and epidermal growth factor receptor family members share parallel activation mechanisms	29
Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations	28
Crosslinking mass spectrometry: A link between structural biology and systems biology	28
Integrative structure and function of the yeast exocyst complex	27
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	27
A glimpse into the molecular mechanism of integral membrane proteins through hydrogen–deuterium exchange mass spectrometry	26
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data	26
Self‐assembling peptides: From a discovery in a yeast protein to diverse uses and beyond	25
Protein folding ‐ seeing is deceiving	25
N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma	25
Templates for writing PyMOL scripts	24
Cumulative deamidations of the major lens protein γS‐crystallin increase its aggregation during unfolding and oxidation	24
Unveiling the binding mode of perfluorooctanoic acid to human serum albumin	23
How bilayer properties influence membrane protein folding	23
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D	23
Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation	22
MMM: Integrative ensemble modeling and ensemble analysis	22
Cryo‐electron microscopy structure of human ABCB6 transporter	22
Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification	22
Evaluation of AlphaFold2 structures as docking targets	22
Electrostatic modulation of hnRNPA1 low‐complexity domain liquid–liquid phase separation and aggregation	22
Three‐dimensional organization of the cytoskeleton: A cryo‐electron tomography perspective	22
Mapping p38α mitogen‐activated protein kinase signaling by proximity‐dependent labeling	21
Initiation of focal adhesion assembly by talin and kindlin: A dynamic view	20

The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes	20
Structural basis for the interaction of SARS‐CoV‐2 virulence factor nsp1 with DNA polymerase α–primase	20
Re‐examining how Munc13‐1 facilitates opening of syntaxin‐1	20
Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models	19
FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains	19
Prokaryote toxin–antitoxin modules: Complex regulation of an unclear function	19
The mechanism of Single strand binding protein–RecG binding: Implications for SSB interactome function	19
The metastable states of proteins	19
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	19
Measuring gas vesicle dimensions by electron microscopy	19
DNA‐binding domain as the minimal region driving RNA‐dependent liquid–liquid phase separation of androgen receptor	19
Small heat shock protein 22 kDa can modulate the aggregation and liquid–liquid phase separation behavior of tau	18
Cryptochromes: Photochemical and structural insight into magnetoreception	18
Deuteration of nonexchangeable protons on proteins affects their thermal stability, side‐chain dynamics, and hydrophobicity	18
CMM—An enhanced platform for interactive validation of metal binding sites	18
Vitamin D and COVID‐19: A review on the role of vitamin D in preventing and reducing the severity of COVID‐19 infection	18
Consensus mutagenesis approach improves the thermal stability of system xc− transporter, xCT, and enables cryo‐EM analyses	18
Characterization of CaMKIIα holoenzyme stability	18
High‐resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels	18
Structural and biochemical characterization of SADS‐CoV papain‐like protease 2	18
Arginine multivalency stabilizes protein/RNA condensates	17
CTD of SARS‐CoV‐2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation	17
ATP regulates RNA‐driven cold inducible RNA binding protein phase separation	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	16
BayeStab: Predicting effects of mutations on protein stability with uncertainty quantification	15
DPAM: A domain parser for AlphaFold models	15
Nucleocytoplasmic transport of intrinsically disordered proteins studied by high‐speed super‐resolution microscopy	15
Computational design of mixed chirality peptide macrocycles with internal symmetry	15
Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement	15
AlphaFold predicts the most complex protein knot and composite protein knots	15
A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer	15
These motors were made for walking	15
Molecular insights into the primary nucleation of polymorphic amyloid β dimers in DOPC lipid bilayer membrane	15
Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay	15
Thioesterase enzyme families: Functions, structures, and mechanisms	15
A systematic analysis of the beta hairpin motif in the Protein Data Bank	14
De novo protein design by inversion of the AlphaFold structure prediction network	14
Crystal structure of SARS‐CoV‐2 nsp10–nsp16 in complex with small molecule inhibitors, SS148 and WZ16	14
Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain	14
PAINT using proteins: A new brush for super‐resolution artists	14
Discriminating changes in protein structure using tyrosine conjugation	14
The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX‐MS, DSC, and nanoDSF	14
The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove	14
Local sequence‐structure relationships in proteins	14
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	14
Mechanisms of protein evolution	14
Molecular basis of the interaction of Hsp90 with its co‐chaperone Hop	14
Resolving the enthalpy of protein stabilization by macromolecular crowding	14
Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase	14
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes	14
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	14
A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices	13
CyDisCo production of functional recombinant SARS‐CoV‐2 spike receptor binding domain	13
Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models	13
Protection by desiccation‐tolerance proteins probed at the residue level	13
AlphaFold predicts novel human proteins with knots	13
New covalent bonding ability for proteins	13
Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana	13
Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions	13
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library	13
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	13
Cyclic nucleotide selectivity of protein kinase G isozymes	12
Nicking and fragmentation are responsible for α‐lactalbumin amyloid fibril formation at acidic pH and elevated temperature	12
The regulation of DNA supercoiling across evolution	12
Flash properties of Gaussia luciferase are the result of covalent inhibition after a limited number of cycles	12
Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates	12
Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7	12
Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein	12
Nonstructural protein 7 and 8 complexes of SARS‐CoV‐2	12
A cellular perspective of bias at G protein‐coupled receptors	12
Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation	12
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	12
Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein	11
Frontotemporal dementia‐linked P112H mutation of TDP‐43 induces protein structural change and impairs its RNA binding function	11
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	11
InteBac: An integrated bacterial and baculovirus expression vector suite	11
Three‐repeat and four‐repeat tau isoforms form different oligomers	11
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	11
Complementing machine learning‐based structure predictions with native mass spectrometry	11
AMP‐BERT: Prediction of antimicrobial peptide function based on a BERT model	11

Cryo‐electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans	10
Structural basis for thioredoxin isoform‐based fine‐tuning of ferredoxin‐thioredoxin reductase activity	10
Ab initio folding of a trefoil‐fold motif reveals structural similarity with a β‐propeller blade motif	10
Substitution scoring matrices for proteins ‐ An overview	10
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	10
Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence	10
Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor	10
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	10
Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin	10
Assessing and enhancing foldability in designed proteins	10
CHARMM‐GUIhigh‐throughput simulator for efficient evaluation of protein–ligand interactions with different force fields	10
Differences in the dynamics of the tandem‐SH2 modules of the Syk and ZAP‐70 tyrosine kinases	9
Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization	9
Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA	9
Differences in stability and calcium sensitivity of the Ig domains in titin's N2A region	9
Estimating conformational heterogeneity of tryptophan synthase with a template‐based Alphafold2 approach	9
Water‐mediated interactions destabilize proteins	9
Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint	9
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation	9
Python‐based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier–Bessel indexing of electron microscopic data	9
Purification and crystal structure of human ODA16: Implications for ciliary import of outer dynein arms by the intraflagellar transport machinery	9
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry	9
PDBsum1: A standalone program for generating PDBsum analyses	9
Stability profile of vimentin rod domain	9
Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	9
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	9
Discovery of antimicrobial agent targeting tryptophan synthase	9
In vivo liquid–liquid phase separation protects amyloidogenic and aggregation‐prone peptides during overexpression in Escherichia coli	9
Molecular insights into α‐synuclein interaction with individual human core histones, linker histone, and dsDNA	9
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	9
Allostery‐driven changes in dynamics regulate the activation of bacterial copper transcription factor	9
The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA‐binding proteins for liquid–liquid phase separation	8
Structural analysis and reaction mechanism of the disproportionating enzyme (D‐enzyme) from potato	8
An apparent core/shell architecture of polyQ aggregates in the aging Caenorhabditis elegans neuron	8
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins	8
Compendium of causative genes and their encoded proteins for common monogenic disorders	8
Cardiolipin interacts with beta‐2‐glycoprotein I and forms an open conformation–Mechanisms analyzed using hydrogen/deuterium exchange	8
Biomolecular phase separation through the lens of sodium‐23 NMR	8
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	8
Biochemical analysis of a sugar 4,6‐dehydratase from Acanthamoeba polyphaga Mimivirus	8
Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans	8
Distinguishing features of fold‐switching proteins	8
Heterologous expression of naturally evolved putative de novo proteins with chaperones	8
Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors	8
Similar protein segments shared between domains of different evolutionary lineages	8
Simple mechanisms for the evolution of protein complexity	8
Predictable fold switching by theSARS‐CoV‐2 proteinORF9b	8
The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis	8
Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase	8
The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases	8
High affinity between CREBBP/p300 and NCOA evolved in vertebrates	8
Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering	7
Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation	7
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods	7
Two fatty acid‐binding proteins expressed in the intestine interact differently with endocannabinoids	7
How enzymes harness highly unfavorable proton transfer reactions	7
Revisiting the phosphotyrosine binding pocket of Fyn SH2 domain led to the identification of novel SH2 superbinders.	7
NF‐κB Rel subunit exchange on a physiological timescale	7
Structural insights into the tropomodulin assembly at the pointed ends of actin filaments	7
Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut	7
Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane	7
Structure of the human Ccr4‐Not nuclease module using X‐ray crystallography and electron paramagnetic resonance spectroscopy distance measurements	7
The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function	7
Crystal structure of the anti‐CRISPR, AcrIIC4	7
Ca2+‐dependent interactions between lipids and the tumor‐targeting peptide pHLIP	7
Structural dynamics of the complex of calmodulin with a minimal functional construct of eukaryotic elongation factor 2 kinase and the role of Thr348 autophosphorylation	7
The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z	7
Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli	7
Extension of a de novo TIM barrel with a rationally designed secondary structure element	7
Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes	7
A newly introduced salt bridge cluster improves structural and biophysical properties of de novoTIM barrels	7
Tertiary motifs as building blocks for the design of protein‐binding peptides	7
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates	7
Intrinsic protein disorder uncouples affinity from binding specificity	7
Innovation and tinkering in the evolution of oxidases	7
Structure‐based design of a photoswitchable affibody scaffold	7
Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid	7
Structural basis of strict substrate recognition of l‐lysine α‐oxidase from Trichoderma viride	7
Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif	7
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	7
Aromaticity at position 39 in α‐synuclein: A modulator of amyloid fibril assembly and membrane‐bound conformations	7
Development of in vivo HDX‐MS with applications to a TonB‐dependent transporter and other proteins	7
Development and characterization of specific anti‐Usutu virus chicken‐derived single chain variable fragment antibodies	7
Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4	7
High‐efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices	7
Shape shifting: The multiple conformational substates of the PTEN N‐terminal PIP2‐binding domain	6
High‐throughput cell‐free screening of eukaryotic membrane protein expression in lipidic mimetics	6
High resolution electron tomography and segmentation‐by‐modeling interpretation in Bsoft	6
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	6
Conserved buried water molecules enable the β‐trefoil architecture	6
Crystal structure of a GH1 β‐glucosidase from Hamamotoa singularis	6
Epitope mapping of novel monoclonal antibodies to human angiotensin I‐converting enzyme	6
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	6
A hierarchical deep learning based approach for multi‐functional enzyme classification	6
Structural investigation of 2‐naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site	6