Protein Science

Article	Citations
UCSF ChimeraX: Structure visualization for researchers, educators, and developers	4755
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions	807
PANTHER: Making genome‐scale phylogenetics accessible to all	546
KEGG mapping tools for uncovering hidden features in biological data	375
Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2	272
DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations	246
DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data	216
The Bio3D packages for structural bioinformatics	206
Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein	200
UCSF ChimeraX: Tools for structure building and analysis	193
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants	146
DALI shines a light on remote homologs: One hundred discoveries	142
The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis	106
The Human Protein Atlas—Spatial localization of the human proteome in health and disease	104
Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences	101
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0	98
Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins	95
The AutoDock suite at 30	92
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D	88
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf	86
Leginon: New features and applications	82
Nanodiscs: A toolkit for membrane protein science	80
Characterization of the SARS‐CoV‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors	70
AlphaFold2 fails to predict protein fold switching	70
DIALS as a toolkit	63

Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease	62
PANNZER—A practical tool for protein function prediction	59
PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system	58
Interplay between tau and α‐synuclein liquid–liquid phase separation	53
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
PDBsum extras: SARS‐CoV‐2 and AlphaFold models	45
Structural and functional understanding of the toll‐like receptors	45
Intrinsic protein disorder and conditional folding in AlphaFoldDB	45
How to use the MEROPS database and website to help understand peptidase specificity	44
Progress toward Alzheimer's disease treatment: Leveraging the Achilles' heel of Aβ oligomers?	44
BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models	43
PDB‐101: Educational resources supporting molecular explorations through biology and medicine	42
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8	41
NMR hawk‐eyed view of AlphaFold2 structures	39
Rapid prediction and analysis of protein intrinsic disorder	38
In‐depth interrogation of protein thermal unfolding data with MoltenProt	36
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps	36
Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms	35
The evolution of the antimicrobial peptide database over 18 years: Milestones and new features	34
ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX	34
Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure	34
Liquid–liquid phase separation of Tau by self and complex coacervation	33
Templates for writing PyMOL scripts	30
Crosslinking mass spectrometry: A link between structural biology and systems biology	30
Integrative structure and function of the yeast exocyst complex	29
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D	28
Evaluation of AlphaFold2 structures as docking targets	28
Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations	28
Unveiling the binding mode of perfluorooctanoic acid to human serum albumin	28
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data	27
N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma	27
Self‐assembling peptides: From a discovery in a yeast protein to diverse uses and beyond	27
Protein folding ‐ seeing is deceiving	25
How bilayer properties influence membrane protein folding	25
Structural basis for the interaction of SARS‐CoV‐2 virulence factor nsp1 with DNA polymerase α–primase	25
Three‐dimensional organization of the cytoskeleton: A cryo‐electron tomography perspective	25
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
Cryo‐electron microscopy structure of human ABCB6 transporter	23
CMM—An enhanced platform for interactive validation of metal binding sites	23
MMM: Integrative ensemble modeling and ensemble analysis	23
CTD of SARS‐CoV‐2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation	22
Characterization of CaMKIIα holoenzyme stability	22
The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes	22
Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation	22
Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification	22
Prokaryote toxin–antitoxin modules: Complex regulation of an unclear function	21

Measuring gas vesicle dimensions by electron microscopy	21
Deuteration of nonexchangeable protons on proteins affects their thermal stability, side‐chain dynamics, and hydrophobicity	20
Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease	20
FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains	20
Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models	20
Initiation of focal adhesion assembly by talin and kindlin: A dynamic view	20
Consensus mutagenesis approach improves the thermal stability of system xc− transporter, xCT, and enables cryo‐EM analyses	19
Small heat shock protein 22 kDa can modulate the aggregation and liquid–liquid phase separation behavior of tau	19
DNA‐binding domain as the minimal region driving RNA‐dependent liquid–liquid phase separation of androgen receptor	19
Resolving the enthalpy of protein stabilization by macromolecular crowding	19
De novo protein design by inversion of the AlphaFold structure prediction network	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
BayeStab: Predicting effects of mutations on protein stability with uncertainty quantification	18
Cryptochromes: Photochemical and structural insight into magnetoreception	18
ATP regulates RNA‐driven cold inducible RNA binding protein phase separation	18
Thioesterase enzyme families: Functions, structures, and mechanisms	18
Crystal structure of SARS‐CoV‐2 nsp10–nsp16 in complex with small molecule inhibitors, SS148 and WZ16	17
Molecular insights into the primary nucleation of polymorphic amyloid β dimers in DOPC lipid bilayer membrane	17
A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer	17
Arginine multivalency stabilizes protein/RNA condensates	17
Molecular basis of the interaction of Hsp90 with its co‐chaperone Hop	16
AlphaFold predicts the most complex protein knot and composite protein knots	16
Computational design of mixed chirality peptide macrocycles with internal symmetry	16
A systematic analysis of the beta hairpin motif in the Protein Data Bank	16
Cyclic nucleotide selectivity of protein kinase G isozymes	16
Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase	16
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
EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components	16
Discriminating changes in protein structure using tyrosine conjugation	15
AlphaFold predicts novel human proteins with knots	15
AMP‐BERT: Prediction of antimicrobial peptide function based on a BERT model	15
RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding	15
The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX‐MS, DSC, and nanoDSF	15
New covalent bonding ability for proteins	15
Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain	15
DPAM: A domain parser for AlphaFold models	15
Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay	15
These motors were made for walking	15
A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices	14
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library	14
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes	14
Nonstructural protein 7 and 8 complexes of SARS‐CoV‐2	14
Local sequence‐structure relationships in proteins	14
Protection by desiccation‐tolerance proteins probed at the residue level	14
The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove	14
PAINT using proteins: A new brush for super‐resolution artists	14
Expanding the family of extracellular chaperones: Identification of human plasma proteins with chaperone activity	14
Frontotemporal dementia‐linked P112H mutation of TDP‐43 induces protein structural change and impairs its RNA binding function	13
Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models	13
Similar protein segments shared between domains of different evolutionary lineages	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
Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint	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
CyDisCo production of functional recombinant SARS‐CoV‐2 spike receptor binding domain	13
Cryo‐electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans	13
Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana	13
Flash properties of Gaussia luciferase are the result of covalent inhibition after a limited number of cycles	12
Distinguishing features of fold‐switching proteins	12
Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates	12
Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation	12
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models	12
Complementing machine learning‐based structure predictions with native mass spectrometry	12
In vivo liquid–liquid phase separation protects amyloidogenic and aggregation‐prone peptides during overexpression in Escherichia coli	12
Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein	12
Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein	12
InteBac: An integrated bacterial and baculovirus expression vector suite	12
Substitution scoring matrices for proteins ‐ An overview	12
Three‐repeat and four‐repeat tau isoforms form different oligomers	11
Rapid directed molecular evolution of fluorescent proteins in mammalian cells	11
CHARMM‐GUIhigh‐throughput simulator for efficient evaluation of protein–ligand interactions with different force fields	11
Exploring the pH dependence of the SARS‐CoV‐2 complete fusion domain and the role of its unique structural features	11
Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin	11
Stability profile of vimentin rod domain	11
Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery	11
Secondary structure and stability of a gel‐forming tardigrade desiccation‐tolerance protein	10
Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence	10

Development of in vivo HDX‐MS with applications to a TonB‐dependent transporter and other proteins	10
Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans	10
PDBsum1: A standalone program for generating PDBsum analyses	10
Structural basis for thioredoxin isoform‐based fine‐tuning of ferredoxin‐thioredoxin reductase activity	10
Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA	10
Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor	10
Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization	10
An apparent core/shell architecture of polyQ aggregates in the aging Caenorhabditis elegans neuron	10
Assessing and enhancing foldability in designed proteins	10
Extension of a de novo TIM barrel with a rationally designed secondary structure element	9
Discovery of antimicrobial agent targeting tryptophan synthase	9
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry	9
The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases	9
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods	9
Water‐mediated interactions destabilize proteins	9
Simple mechanisms for the evolution of protein complexity	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
Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut	9
Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors	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
High affinity between CREBBP/p300 and NCOA evolved in vertebrates	9
Contributions of the N‐terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA‐induced phase separation	9
Differences in the dynamics of the tandem‐SH2 modules of the Syk and ZAP‐70 tyrosine kinases	9
Time Resolved‐Fluorescence Resonance Energy Transfer platform for quantitative nucleosome binding and footprinting	9
Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations	9
Molecular insights into α‐synuclein interaction with individual human core histones, linker histone, and dsDNA	9
Estimating conformational heterogeneity of tryptophan synthase with a template‐based Alphafold2 approach	9
Allostery‐driven changes in dynamics regulate the activation of bacterial copper transcription factor	9
CSM‐peptides: A computational approach to rapid identification of therapeutic peptides	9
SPI “sandwich”: Combined SUMO‐Peptide‐Intein expression system and isolation procedure for improved stability and yield of peptides	9
Revisiting the phosphotyrosine binding pocket of Fyn SH2 domain led to the identification of novel SH2 superbinders.	8
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern	8
A newly introduced salt bridge cluster improves structural and biophysical properties of de novoTIM barrels	8
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins	8
Design and optimization of enzymatic activity in a de novo β‐barrel scaffold	8
Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family	8
Ca2+‐dependent interactions between lipids and the tumor‐targeting peptide pHLIP	8
Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation	8
Computed cancer interactome explains the effects of somatic mutations in cancers	8
Predictable fold switching by theSARS‐CoV‐2 proteinORF9b	8
Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase	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
Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid	8
Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli	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
Structural analysis and reaction mechanism of the disproportionating enzyme (D‐enzyme) from potato	8
Structural basis for substrate specificity of l‐methionine decarboxylase	8
The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis	8
Heterologous expression of naturally evolved putative de novo proteins with chaperones	8
Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation	8
Biomolecular phase separation through the lens of sodium‐23 NMR	8
A hierarchical deep learning based approach for multi‐functional enzyme classification	8
TSGIT: An N‐ and C‐terminal tandem tag system for purification of native and intein‐mediated ligation‐ready proteins	7
Structural basis of strict substrate recognition of l‐lysine α‐oxidase from Trichoderma viride	7
The human protein atlas—Integrated omics for single cell mapping of the human proteome	7
QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets	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
A new strategy to reconcile amyloid cross‐seeding and amyloid prevention in a binary system of α‐synuclein fragmental peptide and hIAPP	7
Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane	7
Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3	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
Innovation and tinkering in the evolution of oxidases	7
Pulse‐field gradient nuclear magnetic resonance of protein translational diffusion from native to non‐native states	7
Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination	7
Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif	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
A genetically encoded far‐red fluorescent calcium ion biosensor derived from a biliverdin‐binding protein	7
How enzymes harness highly unfavorable proton transfer reactions	7
HDOCK update for modeling protein‐RNA/DNA complex structures	7
NKp46‐specific single domain antibodies enable facile engineering of various potent NK cell engager formats	7
Randomized gates eliminate bias in sort‐seq assays	7
Tertiary motifs as building blocks for the design of protein‐binding peptides	7
Crystal structure of the anti‐CRISPR, AcrIIC4	7
Drivers of Hsp104 potentiation revealed by scanning mutagenesis of the middle domain	7
Structure‐based design of a photoswitchable affibody scaffold	7
Uniform binding and negative catalysis at the origin of enzymes	7
The roles of highly conserved, non‐catalytic residues in class A β‐lactamases	7
Phenotypic mutations contribute to protein diversity and shape protein evolution	7
A new kid in the folding funnel: Molecular chaperone activities of the BRICHOS domain	7
Capturing the geometry, function, and evolution of enzymes with 3D templates	7
Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes	7
Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase	7
Structural motifs in protein cores and at protein–protein interfaces are different	7
NF‐κB Rel subunit exchange on a physiological timescale	7
Development and characterization of specific anti‐Usutu virus chicken‐derived single chain variable fragment antibodies	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 of the human Ccr4‐Not nuclease module using X‐ray crystallography and electron paramagnetic resonance spectroscopy distance measurements	7
Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering	7
The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z	7
Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes	7