Current Opinion in Structural Biology

Article	Citations
Machine learning approaches for analyzing and enhancing molecular dynamics simulations	166
Cryo-EM structures of tau filaments	164
How do intrinsically disordered protein regions encode a driving force for liquid–liquid phase separation?	163
Toward better drug discovery with knowledge graph	109
Physics-based computational and theoretical approaches to intrinsically disordered proteins	99
NEDD8 and ubiquitin ligation by cullin-RING E3 ligases	91
Advances in machine learning for directed evolution	86
Respiratory complex I — structure, mechanism and evolution	78
Deep learning techniques have significantly impacted protein structure prediction and protein design	75
Recent advances in glycoinformatic platforms for glycomics and glycoproteomics	73
Principles of nucleosome recognition by chromatin factors and enzymes	73
Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior	72
Ancestral sequence reconstruction for protein engineers	71
Recent results in time resolved serial femtosecond crystallography at XFELs	71
Allosteric drugs and mutations: chances, challenges, and necessity	68
Transcription through the nucleosome	66
Glycan structures and their interactions with proteins. A NMR view	65
Amyloid aggregation simulations: challenges, advances and perspectives	64
Serial synchrotron crystallography for time-resolved structural biology	63
Polarisable force fields: what do they add in biomolecular simulations?	62
NMR illuminates intrinsic disorder	60
Recent trends in peptide and protein-based hydrogels	60
Cryo-electron microscopy analysis of small membrane proteins	57
Deep learning approaches for de novo drug design: An overview	55
Recent progress in molecular simulation methods for drug binding kinetics	54

Enzyme evolution and the temperature dependence of enzyme catalysis	54
Graph neural network approaches for drug-target interactions	52
Structural features of activated GPCR signaling complexes	51
Designing better enzymes: Insights from directed evolution	50
Adaptive machine learning for protein engineering	50
Advances in the calculation of binding free energies	49
Structure and function of naturally evolved de novo proteins	49
Molecular dynamics simulations of DNA–DNA and DNA–protein interactions	49
Epistasis and intramolecular networks in protein evolution	47
Overview of the centriole architecture	47
Structure and function of adenylyl cyclases, key enzymes in cellular signaling	47
How the centriole builds its cilium: of mothers, daughters, and the acquisition of appendages	47
Artificial intelligence challenges for predicting the impact of mutations on protein stability	46
AlphaFold illuminates half of the dark human proteins	45
Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance	43
Beyond structure: emerging approaches to study GPCR dynamics	43
Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins	43
Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids	42
Structural basis of CRISPR-Cas Type III prokaryotic defence systems	42
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity	41
Recent insights into the structure of TFIID, its assembly, and its binding to core promoter	41
Deep generative modeling for protein design	40
Dynamic multivalent interactions of intrinsically disordered proteins	40
How low can we go? Structure determination of small biological complexes using single-particle cryo-EM	40
New insights into no-go, non-stop and nonsense-mediated mRNA decay complexes	39
Understanding the 26S proteasome molecular machine from a structural and conformational dynamics perspective	38
Structural variations of photosystem I-antenna supercomplex in response to adaptations to different light environments	38
Web-based tools for computational enzyme design	38
Structural interconversions of the anaphase-promoting complex/cyclosome (APC/C) regulate cell cycle transitions	38
Spike-heparan sulfate interactions in SARS-CoV-2 infection	38
Structural basis of ergothioneine biosynthesis	38
Different mechanisms for translocation by monomeric and hexameric helicases	37
Protein-complex stability in cells and in vitro under crowded conditions	37
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM	37
Structure and unique mechanical aspects of nuclear lamin filaments	37
Histone chaperone FACT FAcilitates Chromatin Transcription: mechanistic and structural insights	36
Biophysical studies of phase separation integrating experimental and computational methods	36
Structure of respiratory complex I – An emerging blueprint for the mechanism	36
Practically useful protein-design methods combining phylogenetic and atomistic calculations	36
Advances to tackle backbone flexibility in protein docking	36
Structural basis for PRC2 engagement with chromatin	36
INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling	36
Mechanisms of substrate recognition by the 26S proteasome	35
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	35
Multicolor single-molecule FRET for DNA and RNA processes	35
Evolution, folding, and design of TIM barrels and related proteins	34
Structural biology of endogenous membrane protein assemblies in native nanodiscs	34
Everything is connected: Graph neural networks	34
Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins	33
Centrosome organization and functions	33

Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues	32
Modeling conformational states of proteins with AlphaFold	32
Advances in computational structure-based antibody design	32
Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods	32
Glycoproteomics: growing up fast	32
Exploring protein conformations in vitro and in cell with EPR distance measurements	32
Stopping the beating heart of cancer: KRAS reviewed	32
Advances in the study of GPCRs by 19F NMR	31
Structure-based drug design with geometric deep learning	31
Histone tails as signaling antennas of chromatin	31
RUVBL1–RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions	30
The role of water in ligand binding	30
Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly	30
Phase separation in transcription factor dynamics and chromatin organization	30
Systematic design of biomolecular force fields	30
Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation	30
Surfing the wave of oxyfunctionalization chemistry by engineering fungal unspecific peroxygenases	30
Structures and regulations of ATM and ATR, master kinases in genome integrity	30
Allostery of multidomain proteins with disordered linkers	29
Post-translational modification of RAS proteins	29
Challenges in protein docking	29
Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes	29
Structure and engineering of tandem repeat lectins	29
Data-driven computational protein design	29
Illuminating the complexity of GPCR pathway selectivity – advances in biosensor development	29
Artificial protein cages – inspiration, construction, and observation	29
Progress at protein structure prediction, as seen in CASP15	28
DNA methylation: Precise modulation of chromatin structure and dynamics	28
Dynamic protein interfaces and conformational landscapes of membrane protein complexes	28
What do we know about DNA mechanics so far?	27
Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling?	27
Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective	27
AAA+ ATPases: structural insertions under the magnifying glass	27
Advances in molecular simulations of protein mechanical properties and function	27
Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics	27
Principles of SARS-CoV-2 glycosylation	27
Nucleosome positioning and chromatin organization	27
Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models	27
Multiscale simulation approaches to modeling drug–protein binding	27
Emerging structural insights into GPCR–β-arrestin interaction and functional outcomes	26
Centrosomes in disease: how the same music can sound so different?	26
Computational methods to predict protein aggregation	26
Winning the numbers game in enzyme evolution – fast screening methods for improved biotechnology proteins	26
RNA helicases are hubs that orchestrate exosome-dependent 3′–5′ decay	26
Centrosomes in mitotic spindle assembly and orientation	26
Accessorizing the centrosome: new insights into centriolar appendages and satellites	26
P4-ATPases: how an old dog learnt new tricks — structure and mechanism of lipid flippases	25
Ras assemblies and signaling at the membrane	25
Uncovering post-translational modification-associated protein–protein interactions	25
Modes of allosteric regulation of the ubiquitination machinery	25
The ugly, bad, and good stories of large-scale biomolecular simulations	25
Recent advances and current trends in cryo-electron microscopy	25
Allostery in membrane proteins	24
Machine learned coarse-grained protein force-fields: Are we there yet?	24
Emerging patterns of tyrosine sulfation and O-glycosylation cross-talk and co-localization	24
Multiscale modelling and simulation of viruses	24
Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions	24
Unifying coarse-grained force fields for folded and disordered proteins	24
Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms	24
Novel nucleocytoplasmic protein O-fucosylation by SPINDLY regulates diverse developmental processes in plants	24
Advances in optimizing enzyme electrostatic preorganization	24
Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage	24
Integrating cryo-EM and NMR data	23
Transcription factor binding kinetics and transcriptional bursting: What do we really know?	23
The mannose receptor ligands and the macrophage glycome	23
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	23
AlphaFold2 protein structure prediction: Implications for drug discovery	23
Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries	23
Allostery in C-type lectins	23
Generative deep learning for macromolecular structure and dynamics	23
Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?	22
Protein topology and allostery	22
Megadalton chromatin remodelers: common principles for versatile functions	22
Ton motor complexes	22
Fragment molecular orbital calculations for biomolecules	22
Mannosidase mechanism: at the intersection of conformation and catalysis	22
Computational structure modeling for diverse categories of macromolecular interactions	21
Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation	21
An integrated view of p53 dynamics, function, and reactivation	21
Probing membrane protein–lipid interactions	21

Protein structural dynamics by Magic-Angle Spinning NMR	21
Structure-based mechanistic insights into catalysis by tRNA thiolation enzymes	21
Enzyme promiscuity of carbohydrate active enzymes and their applications in biocatalysis	21
Small molecule protein binding to correct cellular folding or stabilize the native state against misfolding and aggregation	21
Local resolution estimates of cryoEM reconstructions	21
Dynamical reweighting methods for Markov models	21
The structure of the γ-TuRC: a 25-years-old molecular puzzle	20
Antibody recognition of bacterial surfaces and extracellular polysaccharides	20
Artificial intelligence in multi-objective drug design	20
Regulation of the multisubunit CCR4-NOT deadenylase in the initiation of mRNA degradation	20
Design and engineering of allosteric communications in proteins	20
Design principles of protein switches	20
Dynamical spectroscopy and microscopy of proteins in cells	19
Unraveling linker histone interactions in nucleosomes	19
Structural overview of macromolecular machines involved in ribosome biogenesis	19
Quantitative characterization of O-GalNAc glycosylation	19
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics	19
Protein assembly and crowding simulations	19
Structural studies of the spliceosome: Bridging the gaps	19
Deep learning methods for 3D structural proteome and interactome modeling	19
Herpesvirus membrane fusion – a team effort	19
Engineering Cas9 for human genome editing	19
Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining	19
Unraveling protein’s structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies	18
Microfluidics and the quantification of biomolecular interactions	18
Mass spectrometry hybridized with gas-phase InfraRed spectroscopy for glycan sequencing	18
Recent advances in single-molecule fluorescence microscopy render structural biology dynamic	18
Docking approaches for modeling multi-molecular assemblies	18
Halogenases: structures and functions	18
Membrane protein folding and quality control	18
High throughput and quantitative enzymology in the genomic era	18
SOD1 oligomers in amyotrophic lateral sclerosis	18
Implications of disease-related mutations at protein–protein interfaces	17
Assembly of RNA polymerase II transcription initiation complexes	17
Transient state measurements on proteins by time-resolved crystallography	17
How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation	17
Constant pH molecular dynamics simulations: Current status and recent applications	17
Nucleosome unwrapping and unstacking	17
Modeling glycosaminoglycan–protein complexes	17
Design and discovery of metamorphic proteins	17
Structural insights into DNA loop extrusion by SMC protein complexes	17
Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding	17
Chemical language models for de novo drug design: Challenges and opportunities	16
Developments in describing equilibrium phase transitions of multivalent associative macromolecules	16
Artificial intelligence based methods for hot spot prediction	16
Discovery of allosteric binding sites by crystallographic fragment screening	16
Setting the stage for evolution of a new enzyme	16
Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions	16
Recent progress in general force fields of small molecules	16
Integrating structure-based approaches in generative molecular design	16
Protein-based functional hybrid bionanomaterials by bottom-up approaches	16
Non-adaptive complexity and biochemical function	16
Glycosylation as a key parameter in the design of nucleic acid vaccines	16
The conformational transition during G protein–coupled receptor (GPCR) and G protein interaction	15
Structural glycobiology in the age of electron cryo-microscopy	15
Chromatin structure changes during various processes from a DNA sequence view	15
Beyond protein structure determination with MicroED	15
In-cell NMR: From target structure and dynamics to drug screening	15
Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs	15
From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology	15
Visualization of intrinsically disordered proteins by high-speed atomic force microscopy	15
Computational approaches to predict protein functional families and functional sites	15
Unveiling induced folding of intrinsically disordered proteins – Protein engineering, frustration and emerging themes	15
The material state of centrosomes: lattice, liquid, or gel?	15
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	15
Searching protein space for ancient sub-domain segments	15
Capturing the mechanics of clathrin-mediated endocytosis	15
Myomics: myosin VI structural and functional plasticity	15
Cell guidance ligands, receptors and complexes – orchestrating signalling in time and space	15
TADs: Dynamic structures to create stable regulatory functions	15
Recent progress in designing protein-based supramolecular assemblies	15
Graphs of dynamic H-bond networks: from model proteins to protein complexes in cell signaling	15
Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods	14
Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates?	14
Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts	14
Assembly of eukaryotic photosystem II with diverse light-harvesting antennas	14
Nucleosomes as allosteric scaffolds for genetic regulation	14
Macromolecular complex in recognition and proteolysis of amyloid precursor protein in Alzheimer’s disease	14
Structural insights into N-linked glycan-mediated protein folding from chemical and biological perspectives	14
An emerging mechanism for the maturation of the Small Subunit Processome	14
Recent advances in single-cell epigenomics	14
Use of single-molecule time-series data for refining conformational dynamics in molecular simulations	14
CRISPR adaptation from a structural perspective	14
Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins	14
Glycosaminoglycan interaction networks and databases	14
Emerging insights into symmetry breaking in centriole duplication: updated view on centriole duplication theory	14
Convergent pathways to biosynthesis of the versatile cofactor F420	14
Constructing PCM with architecturally distinct higher-order assemblies	14
Revealing bacterial cell biology using cryo-electron tomography	14
The current structural glycome landscape and emerging technologies	13
The role of local versus nonlocal physicochemical restraints in determining protein native structure	13
Structure and mechanism of the γ-secretase intramembrane protease complex	13
Cryo-electron microscopy of the chromatin fiber	13
Centriole length control	13
Enzymatic methylation of the amide bond	13