Current Opinion in Structural Biology

Article	Citations
How do intrinsically disordered protein regions encode a driving force for liquid–liquid phase separation?	192
Toward better drug discovery with knowledge graph	129
NEDD8 and ubiquitin ligation by cullin-RING E3 ligases	105
Physics-based computational and theoretical approaches to intrinsically disordered proteins	104
Advances in machine learning for directed evolution	104
Principles of nucleosome recognition by chromatin factors and enzymes	92
Ancestral sequence reconstruction for protein engineers	88
Deep learning techniques have significantly impacted protein structure prediction and protein design	86
Recent results in time resolved serial femtosecond crystallography at XFELs	84
Everything is connected: Graph neural networks	81
Deep learning approaches for de novo drug design: An overview	80
Serial synchrotron crystallography for time-resolved structural biology	75
Amyloid aggregation simulations: challenges, advances and perspectives	72
Graph neural network approaches for drug-target interactions	71
Modeling conformational states of proteins with AlphaFold	68
Adaptive machine learning for protein engineering	66
NMR illuminates intrinsic disorder	64
Epistasis and intramolecular networks in protein evolution	61
Designing better enzymes: Insights from directed evolution	61
Artificial intelligence challenges for predicting the impact of mutations on protein stability	61
Deep generative modeling for protein design	59
Enzyme evolution and the temperature dependence of enzyme catalysis	59
Structure-based drug design with geometric deep learning	57
Overview of the centriole architecture	57
Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins	57

Structure and function of naturally evolved de novo proteins	56
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity	56
AlphaFold illuminates half of the dark human proteins	55
How the centriole builds its cilium: of mothers, daughters, and the acquisition of appendages	53
Advances in computational structure-based antibody design	53
Spike-heparan sulfate interactions in SARS-CoV-2 infection	49
Progress at protein structure prediction, as seen in CASP15	48
Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids	47
Structural basis of CRISPR-Cas Type III prokaryotic defence systems	46
DNA methylation: Precise modulation of chromatin structure and dynamics	46
Web-based tools for computational enzyme design	45
Structure of respiratory complex I – An emerging blueprint for the mechanism	45
Computational methods to predict protein aggregation	45
Structural basis of ergothioneine biosynthesis	43
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	43
New insights into no-go, non-stop and nonsense-mediated mRNA decay complexes	43
Biophysical studies of phase separation integrating experimental and computational methods	43
Phase separation in transcription factor dynamics and chromatin organization	42
Protein-complex stability in cells and in vitro under crowded conditions	41
Structural basis for PRC2 engagement with chromatin	41
Evolution, folding, and design of TIM barrels and related proteins	41
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM	41
Histone chaperone FACT FAcilitates Chromatin Transcription: mechanistic and structural insights	40
Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins	40
Exploring protein conformations in vitro and in cell with EPR distance measurements	39
AlphaFold2 protein structure prediction: Implications for drug discovery	39
RUVBL1–RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions	39
Advances in the study of GPCRs by 19F NMR	39
Advances to tackle backbone flexibility in protein docking	39
Recent advances and current trends in cryo-electron microscopy	39
Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues	38
Mechanisms of substrate recognition by the 26S proteasome	38
The mannose receptor ligands and the macrophage glycome	38
Histone tails as signaling antennas of chromatin	38
The role of water in ligand binding	38
Uncovering post-translational modification-associated protein–protein interactions	37
Surfing the wave of oxyfunctionalization chemistry by engineering fungal unspecific peroxygenases	37
Centrosomes in mitotic spindle assembly and orientation	37
The ugly, bad, and good stories of large-scale biomolecular simulations	37
Glycoproteomics: growing up fast	36
Post-translational modification of RAS proteins	36
Artificial intelligence in multi-objective drug design	36
Stopping the beating heart of cancer: KRAS reviewed	36
Principles of SARS-CoV-2 glycosylation	35
Structural biology of endogenous membrane protein assemblies in native nanodiscs	35
Data-driven computational protein design	35
Illuminating the complexity of GPCR pathway selectivity – advances in biosensor development	35
Multicolor single-molecule FRET for DNA and RNA processes	35
Emerging structural insights into GPCR–β-arrestin interaction and functional outcomes	35
Centrosome organization and functions	35

Machine learned coarse-grained protein force-fields: Are we there yet?	34
Systematic design of biomolecular force fields	34
Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation	34
AAA+ ATPases: structural insertions under the magnifying glass	33
Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective	33
Unifying coarse-grained force fields for folded and disordered proteins	32
Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling?	32
Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes	31
Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics	31
Chemical language models for de novo drug design: Challenges and opportunities	31
TADs: Dynamic structures to create stable regulatory functions	31
Transcription factor binding kinetics and transcriptional bursting: What do we really know?	31
Accessorizing the centrosome: new insights into centriolar appendages and satellites	30
Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms	30
Design principles of protein switches	29
Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries	29
Centrosomes in disease: how the same music can sound so different?	29
Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models	29
Regulation of the multisubunit CCR4-NOT deadenylase in the initiation of mRNA degradation	28
Fragment molecular orbital calculations for biomolecules	28
Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions	28
Novel nucleocytoplasmic protein O-fucosylation by SPINDLY regulates diverse developmental processes in plants	28
Protein assembly and crowding simulations	27
Using machine learning to predict the effects and consequences of mutations in proteins	27
Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation	26
RNA helicases are hubs that orchestrate exosome-dependent 3′–5′ decay	26
Design and engineering of allosteric communications in proteins	26
Capturing the mechanics of clathrin-mediated endocytosis	26
Structural studies of the spliceosome: Bridging the gaps	26
Advances in optimizing enzyme electrostatic preorganization	26
Structures and consequences of pioneer factor binding to nucleosomes	25
Generative deep learning for macromolecular structure and dynamics	25
Structure-based mechanistic insights into catalysis by tRNA thiolation enzymes	25
Engineering Cas9 for human genome editing	25
Constant pH molecular dynamics simulations: Current status and recent applications	25
The structure of the γ-TuRC: a 25-years-old molecular puzzle	25
Small molecule protein binding to correct cellular folding or stabilize the native state against misfolding and aggregation	25
Artificial intelligence based methods for hot spot prediction	25
Integrating structure-based approaches in generative molecular design	24
Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates?	24
Ton motor complexes	24
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	24
Probing membrane protein–lipid interactions	24
Recent advances in single-molecule fluorescence microscopy render structural biology dynamic	24
Protein structural dynamics by Magic-Angle Spinning NMR	24
Discovery of allosteric binding sites by crystallographic fragment screening	23
Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?	23
An integrated view of p53 dynamics, function, and reactivation	23
Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts	22
Microfluidics and the quantification of biomolecular interactions	22
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	22
Quantitative characterization of O-GalNAc glycosylation	22
Dynamical spectroscopy and microscopy of proteins in cells	22
Enzyme promiscuity of carbohydrate active enzymes and their applications in biocatalysis	22
Recent progress in general force fields of small molecules	22
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics	21
SOD1 oligomers in amyotrophic lateral sclerosis	21
Deep learning methods for 3D structural proteome and interactome modeling	21
Unraveling linker histone interactions in nucleosomes	21
CRISPR adaptation from a structural perspective	21
Setting the stage for evolution of a new enzyme	21
Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding	21
Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs	21
Assembly of RNA polymerase II transcription initiation complexes	20
New insights into GPCR coupling and dimerisation from cryo-EM structures	20
Implications of disease-related mutations at protein–protein interfaces	20
Membrane protein folding and quality control	20
From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology	20
Halogenases: structures and functions	20
The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome	20
Visualization of intrinsically disordered proteins by high-speed atomic force microscopy	20
Structural insights into DNA loop extrusion by SMC protein complexes	19
Unraveling protein’s structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies	19
The conformational transition during G protein–coupled receptor (GPCR) and G protein interaction	19
Modeling glycosaminoglycan–protein complexes	19
Artificial intelligence for compound pharmacokinetics prediction	19
Structural and functional roles of 2’-O-ribose methylations and their enzymatic machinery across multiple classes of RNAs	19
High throughput and quantitative enzymology in the genomic era	19
Design and discovery of metamorphic proteins	19
Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods	19

Transient state measurements on proteins by time-resolved crystallography	19
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	19
Structural overview of macromolecular machines involved in ribosome biogenesis	19
Frontiers in the enzymology of thiamin diphosphate-dependent enzymes	19
Non-adaptive complexity and biochemical function	18
Undergraduate structural biology education: A shift from users to developers of computation and simulation tools	18
Unveiling induced folding of intrinsically disordered proteins – Protein engineering, frustration and emerging themes	18
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	18
How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation	18
Searching protein space for ancient sub-domain segments	18
The regulation of the protein interaction network by monoubiquitination	18
Mucin networks: Dynamic structural assemblies controlling mucus function	18
Pondering the mechanism of receptor tyrosine kinase activation: The case for ligand-specific dimer microstate ensembles	18
Developments in describing equilibrium phase transitions of multivalent associative macromolecules	18
Challenges in making ideal cryo-EM samples	18
Computational approaches to predict protein functional families and functional sites	18
Artificial intelligence approaches to human-microbiome protein–protein interactions	18
Structural insights into the interaction between transcription factors and the nucleosome	17
An emerging mechanism for the maturation of the Small Subunit Processome	17
Nucleic acid actions on abnormal protein aggregation, phase transitions and phase separation	17
Revealing bacterial cell biology using cryo-electron tomography	17
Structural insights into N-linked glycan-mediated protein folding from chemical and biological perspectives	17
Progress toward improved understanding of antibody maturation	17
Structure and function of lipid droplet assembly complexes	17
The material state of centrosomes: lattice, liquid, or gel?	17
Glycosaminoglycan interaction networks and databases	17
Structural insights into assembly of transcription preinitiation complex	17
Enhancing sampling with free-energy calculations	17
In-cell NMR: From target structure and dynamics to drug screening	17
Glycosylation as a key parameter in the design of nucleic acid vaccines	17
Myomics: myosin VI structural and functional plasticity	16
Structure and mechanism of the γ-secretase intramembrane protease complex	16
Time-resolved X-ray scattering studies of proteins	16
Structural ensembles of disordered proteins from hierarchical chain growth and simulation	16
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	16
Constructing PCM with architecturally distinct higher-order assemblies	16
Radiation damage to biological macromolecules∗	16
Deep learning for protein complex structure prediction	16
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	16
Computer-aided drug design, quantum-mechanical methods for biological problems	16
Structural insights into the small GTPase specificity of the DOCK guanine nucleotide exchange factors	16
Protein engineering responses to the COVID-19 pandemic	15
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	15
Emerging insights into symmetry breaking in centriole duplication: updated view on centriole duplication theory	15
Emerging structural insights into C-type glycosyltransferases	15
Solving the structural puzzle of bacterial glycome	15
Protein structure prediction in the deep learning era	15
Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases	15
Recent advances in single-cell epigenomics	15
Telomerase structural biology comes of age	15
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis	15
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	15
Information-driven modeling of biomolecular complexes	15
Navigating large chemical spaces in early-phase drug discovery	15
NMR of glycoproteins: profiling, structure, conformation and interactions	15
Genome modeling: From chromatin fibers to genes	15
Dynamic Protein-RNA recognition in primary MicroRNA processing	14
NMR of RNA - Structure and interactions	14
Convergent pathways to biosynthesis of the versatile cofactor F420	14
Anatomy of the fungal microtubule organizing center, the spindle pole body	14
Diffusive intracellular interactions: On the role of protein net charge and functional adaptation	14
The host glycomic response to pathogens	14
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	14
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	14
Federated learning for molecular discovery	14
Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins	14
Structural advances in transcription elongation	14
Awakening of the zygotic genome by pioneer transcription factors	14
Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling	14
Outer membrane protein evolution	14
Protein dynamics by the combination of high-speed AFM and computational modeling	14
Enzymatic methylation of the amide bond	14
Miniature CRISPR-Cas12 endonucleases – Programmed DNA targeting in a smaller package	14
Untangling the complexity of membrane protein folding	14
Structural perspectives on H2S homeostasis	14
Site-specific ubiquitination: Deconstructing the degradation tag	13
Binding and folding in transcriptional complexes	13
Gas-phase infrared spectroscopy of glycans and glycoconjugates	13
Industrializing AI/ML during the end-to-end drug discovery process	13
Centriole length control	13
Toward the equilibrium and kinetics of amyloid peptide self-assembly	13
Integrating experimental data with molecular simulations to investigate RNA structural dynamics	13
Role of aberrant phase separation in pathological protein aggregation	13
Structural determinants of regulated proteolysis in pathogenic bacteria by ClpP and the proteasome	13
Structural biology of SARS-CoV-2 Mpro and drug discovery	13
Mass spectrometry informs the structure and dynamics of membrane proteins involved in lipid and drug transport	13
RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases	13
The role of local versus nonlocal physicochemical restraints in determining protein native structure	13
Structural biology of SMC complexes across the tree of life	12
Combining crystallography with quantum mechanics	12
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	12
Expansion microscopy: A chemical approach for super-resolution microscopy	12
Conserved and divergent mechanisms of inner kinetochore assembly onto centromeric chromatin	12
Toward complete rational control over protein structure and function through computational design	12
Evolution of the centrosome, from the periphery to the center	12