Protein Science

Article	Citations
UCSF ChimeraX: Structure visualization for researchers, educators, and developers	4484
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions	771
PANTHER: Making genome‐scale phylogenetics accessible to all	486
KEGG mapping tools for uncovering hidden features in biological data	359
Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2	268
DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations	239
DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data	203
Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein	197
The Bio3D packages for structural bioinformatics	196
UCSF ChimeraX: Tools for structure building and analysis	136
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants	133
DALI shines a light on remote homologs: One hundred discoveries	114
The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis	102
The Human Protein Atlas—Spatial localization of the human proteome in health and disease	100
Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences	99
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0	88
Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins	86
The AutoDock suite at 30	83
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	83
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	77
Nanodiscs: A toolkit for membrane protein science	77
Leginon: New features and applications	76
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	67
AlphaFold2 fails to predict protein fold switching	66
DIALS as a toolkit	56

PANNZER—A practical tool for protein function prediction	55
PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system	53
Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	53
Interplay between tau and α‐synuclein liquid–liquid phase separation	52
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	47
Multiple sites on SARS‐CoV‐2 spike protein are susceptible to proteolysis by cathepsins B, K, L, S, and V	47
Structural and functional understanding of the toll‐like receptors	45
Progress toward Alzheimer's disease treatment: Leveraging the Achilles' heel of Aβ oligomers?	44
Intrinsic protein disorder and conditional folding in AlphaFoldDB	43
How to use the MEROPS database and website to help understand peptidase specificity	43
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8	41
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	41
PDB‐101: Educational resources supporting molecular explorations through biology and medicine	41
BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models	39
NMR hawk‐eyed view of AlphaFold2 structures	38
Rapid prediction and analysis of protein intrinsic disorder	35
In‐depth interrogation of protein thermal unfolding data with MoltenProt	34
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps	33
Liquid–liquid phase separation of Tau by self and complex coacervation	33
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	32
Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure	31
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	30
Insulin and epidermal growth factor receptor family members share parallel activation mechanisms	29
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	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
N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma	27
Templates for writing PyMOL scripts	27
Self‐assembling peptides: From a discovery in a yeast protein to diverse uses and beyond	27
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data	26
Unveiling the binding mode of perfluorooctanoic acid to human serum albumin	26
Evaluation of AlphaFold2 structures as docking targets	26
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D	25
Protein folding ‐ seeing is deceiving	25
How bilayer properties influence membrane protein folding	24
Cumulative deamidations of the major lens protein γS‐crystallin increase its aggregation during unfolding and oxidation	24
Electrostatic modulation of hnRNPA1 low‐complexity domain liquid–liquid phase separation and aggregation	24
MMM: Integrative ensemble modeling and ensemble analysis	23
Structural basis for the interaction of SARS‐CoV‐2 virulence factor nsp1 with DNA polymerase α–primase	23
Three‐dimensional organization of the cytoskeleton: A cryo‐electron tomography perspective	23
Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification	22
Cryo‐electron microscopy structure of human ABCB6 transporter	22
Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation	22
Characterization of CaMKIIα holoenzyme stability	22
Mapping p38α mitogen‐activated protein kinase signaling by proximity‐dependent labeling	21
The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes	21
Initiation of focal adhesion assembly by talin and kindlin: A dynamic view	20

Deuteration of nonexchangeable protons on proteins affects their thermal stability, side‐chain dynamics, and hydrophobicity	20
Prokaryote toxin–antitoxin modules: Complex regulation of an unclear function	20
Measuring gas vesicle dimensions by electron microscopy	20
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	20
The metastable states of proteins	19
DNA‐binding domain as the minimal region driving RNA‐dependent liquid–liquid phase separation of androgen receptor	19
The mechanism of Single strand binding protein–RecG binding: Implications for SSB interactome function	19
FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains	19
Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models	19
CMM—An enhanced platform for interactive validation of metal binding sites	19
High‐resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels	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
Cryptochromes: Photochemical and structural insight into magnetoreception	18
Small heat shock protein 22 kDa can modulate the aggregation and liquid–liquid phase separation behavior of tau	18
Structural and biochemical characterization of SADS‐CoV papain‐like protease 2	18
CTD of SARS‐CoV‐2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation	17
Arginine multivalency stabilizes protein/RNA condensates	17
Thioesterase enzyme families: Functions, structures, and mechanisms	17
De novo protein design by inversion of the AlphaFold structure prediction network	17
ATP regulates RNA‐driven cold inducible RNA binding protein phase separation	17
BayeStab: Predicting effects of mutations on protein stability with uncertainty quantification	17
Mechanisms of protein evolution	16
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
Computational design of mixed chirality peptide macrocycles with internal symmetry	16
Resolving the enthalpy of protein stabilization by macromolecular crowding	16
Crystal structure of SARS‐CoV‐2 nsp10–nsp16 in complex with small molecule inhibitors, SS148 and WZ16	16
Molecular insights into the primary nucleation of polymorphic amyloid β dimers in DOPC lipid bilayer membrane	16
A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer	16
Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement	15
Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay	15
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	15
Molecular basis of the interaction of Hsp90 with its co‐chaperone Hop	15
AlphaFold predicts the most complex protein knot and composite protein knots	15
These motors were made for walking	15
DPAM: A domain parser for AlphaFold models	15
Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain	15
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	15
Cyclic nucleotide selectivity of protein kinase G isozymes	14
AlphaFold predicts novel human proteins with knots	14
Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase	14
Local sequence‐structure relationships in proteins	14
A systematic analysis of the beta hairpin motif in the Protein Data Bank	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
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library	14
PAINT using proteins: A new brush for super‐resolution artists	14
Discriminating changes in protein structure using tyrosine conjugation	14
Nonstructural protein 7 and 8 complexes of SARS‐CoV‐2	14
New covalent bonding ability for proteins	14
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes	14
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	14
A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices	14
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
Reconstitution and use of highly active human CDK1:Cyclin‐B:CKS1 complexes	13
Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions	13
AMP‐BERT: Prediction of antimicrobial peptide function based on a BERT model	13
Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana	13
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education	13
Nicking and fragmentation are responsible for α‐lactalbumin amyloid fibril formation at acidic pH and elevated temperature	13
The regulation of DNA supercoiling across evolution	13
Protection by desiccation‐tolerance proteins probed at the residue level	13
Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates	12
Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein	12
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	12
A cellular perspective of bias at G protein‐coupled receptors	12
Flash properties of Gaussia luciferase are the result of covalent inhibition after a limited number of cycles	12
Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation	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
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	11
InteBac: An integrated bacterial and baculovirus expression vector suite	11
Three‐repeat and four‐repeat tau isoforms form different oligomers	11
Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin	11
Complementing machine learning‐based structure predictions with native mass spectrometry	11
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	11
In vivo liquid–liquid phase separation protects amyloidogenic and aggregation‐prone peptides during overexpression in Escherichia coli	10
Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	10
Structural basis for thioredoxin isoform‐based fine‐tuning of ferredoxin‐thioredoxin reductase activity	10

Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor	10
PDBsum1: A standalone program for generating PDBsum analyses	10
Cryo‐electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans	10
Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization	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
Substitution scoring matrices for proteins ‐ An overview	10
Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence	10
Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans	10
Discovery of antimicrobial agent targeting tryptophan synthase	9
Distinguishing features of fold‐switching proteins	9
Molecular insights into α‐synuclein interaction with individual human core histones, linker histone, and dsDNA	9
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods	9
Water‐mediated interactions destabilize proteins	9
Similar protein segments shared between domains of different evolutionary lineages	9
Differences in the dynamics of the tandem‐SH2 modules of the Syk and ZAP‐70 tyrosine kinases	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
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	9
Estimating conformational heterogeneity of tryptophan synthase with a template‐based Alphafold2 approach	9
Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors	9
Stability profile of vimentin rod domain	9
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	9
Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA	9
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry	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
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
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern	8
An apparent core/shell architecture of polyQ aggregates in the aging Caenorhabditis elegans neuron	8
Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase	8
Cardiolipin interacts with beta‐2‐glycoprotein I and forms an open conformation–Mechanisms analyzed using hydrogen/deuterium exchange	8
Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid	8
Biomolecular phase separation through the lens of sodium‐23 NMR	8
Simple mechanisms for the evolution of protein complexity	8
Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli	8
Revisiting the phosphotyrosine binding pocket of Fyn SH2 domain led to the identification of novel SH2 superbinders.	8
Development of in vivo HDX‐MS with applications to a TonB‐dependent transporter and other proteins	8
The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis	8
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins	8
Heterologous expression of naturally evolved putative de novo proteins with chaperones	8
High affinity between CREBBP/p300 and NCOA evolved in vertebrates	8
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	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
A hierarchical deep learning based approach for multi‐functional enzyme classification	8
Structural analysis and reaction mechanism of the disproportionating enzyme (D‐enzyme) from potato	8
Predictable fold switching by theSARS‐CoV‐2 proteinORF9b	8
Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut	8
Compendium of causative genes and their encoded proteins for common monogenic disorders	8
The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases	8
Ca2+‐dependent interactions between lipids and the tumor‐targeting peptide pHLIP	8
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
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	8
Phenotypic mutations contribute to protein diversity and shape protein evolution	7
TSGIT: An N‐ and C‐terminal tandem tag system for purification of native and intein‐mediated ligation‐ready proteins	7
How enzymes harness highly unfavorable proton transfer reactions	7
Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif	7
NKp46‐specific single domain antibodies enable facile engineering of various potent NK cell engager formats	7
Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes	7
A new kid in the folding funnel: Molecular chaperone activities of the BRICHOS domain	7
Development and characterization of specific anti‐Usutu virus chicken‐derived single chain variable fragment antibodies	7
A newly introduced salt bridge cluster improves structural and biophysical properties of de novoTIM barrels	7
Design and optimization of enzymatic activity in a de novo β‐barrel scaffold	7
Structure of the human Ccr4‐Not nuclease module using X‐ray crystallography and electron paramagnetic resonance spectroscopy distance measurements	7
Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation	7
Crystal structure of the anti‐CRISPR, AcrIIC4	7
The roles of highly conserved, non‐catalytic residues in class A β‐lactamases	7
Structural basis of strict substrate recognition of l‐lysine α‐oxidase from Trichoderma viride	7
Computed cancer interactome explains the effects of somatic mutations in cancers	7
Extension of a de novo TIM barrel with a rationally designed secondary structure element	7
NF‐κB Rel subunit exchange on a physiological timescale	7
Functional analysis of protein post‐translational modifications using genetic codon expansion	7
Structural insights into the tropomodulin assembly at the pointed ends of actin filaments	7
Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane	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
The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function	7
Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering	7
Two fatty acid‐binding proteins expressed in the intestine interact differently with endocannabinoids	7
Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices	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
Aromaticity at position 39 in α‐synuclein: A modulator of amyloid fibril assembly and membrane‐bound conformations	7
Structural motifs in protein cores and at protein–protein interfaces are different	7
HDOCK update for modeling protein‐RNA/DNA complex structures	7
Randomized gates eliminate bias in sort‐seq assays	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
Structure‐based design of a photoswitchable affibody scaffold	7
Innovation and tinkering in the evolution of oxidases	7
Crystal structure of a GH1 β‐glucosidase from Hamamotoa singularis	6
High resolution electron tomography and segmentation‐by‐modeling interpretation in Bsoft	6
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	6