Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	271
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	193
Editorial	156
Harnessing the 14-3-3 protein–protein interaction network	120
Optogenetic enzymes: A deep dive into design and impact	112
Mutational fitness landscape and drug resistance	107
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	105
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	101
Recent advances in AI-driven pKa prediction for proteins and small molecules	93
Computer-aided drug design, quantum-mechanical methods for biological problems	89
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	87
Raman spectroscopy and imaging of protein droplet formation and aggregation	82
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	82
Genome modeling: From chromatin fibers to genes	81
May the proton motive force be with you: A plant transporter review	79
Catalysis and structure of nitrogenases	79
Next-generation predictors of protein phase behavior	77
Navigating protein–nucleic acid sequence-structure landscapes with deep learning	77
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	76
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	70
Markov field models: Scaling molecular kinetics approaches to large molecular machines	69
Editorial Board	69
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	68
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	66
NMR tools to detect protein allostery	66

Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages	64
Modeling membranes in situ	64
Advancing protein structure prediction beyond AlphaFold2	63
Advances in native cell membrane nanoparticles system	62
Dynamics and interactions of intrinsically disordered proteins	61
Mucin networks: Dynamic structural assemblies controlling mucus function	61
Protein dynamics underlying allosteric regulation	60
Molecular dynamics simulations for the study of chromatin biology	60
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	60
The mannose receptor ligands and the macrophage glycome	59
In situ single-particle Cryo-EM methods: Principle and applications	56
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	56
Conformational penalties: New insights into nucleic acid recognition	56
Therapeutic implications of target residence time	54
Artificial intelligence in therapeutic antibody design: Advances and future prospects	54
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	54
Dynamic interactions drive early spliceosome assembly	53
NMR of RNA - Structure and interactions	53
Table of contents	50
Table of contents	50
Macromolecular assemblies: Molecular mechanisms abound	49
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	48
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	48
Probing protein–DNA interactions and compaction in nanochannels	48
Biomolecular simulations at the exascale: From drug design to organelles and beyond	47
Structural insights into assembly of transcription preinitiation complex	46
Challenges and compromises: Predicting unbound antibody structures with deep learning	46
DDK promotes DNA replication initiation: Mechanistic and structural insights	46
Viral amyloids: New opportunities for antiviral therapeutic strategies	46
The role of RNA structure in 3’ end processing in eukaryotes	46
Microsecond time-resolved cryo-electron microscopy	45
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	45
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	45
Table of contents	44
Cryo-EM diversifies	44
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	44
Structural host immune-microbiota interactions	44
Structural biology in the age of X-ray free-electron lasers and exascale computing	43
Solid-state NMR of membrane proteins in situ	43
The CMG DNA helicase and the core replisome	43
Are N-linked glycans intrinsically disordered?	43
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	42
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	42
Ligand-like lipid interactions with membrane proteins: Simulations and machine learning	42
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	42
Nuclear periphery and its mechanical regulation in cell fate transitions	42
Integrating cellular and molecular structures and dynamics into whole-cell models	41
Frustration, dynamics, and catalysis	40
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	40
Insights in bacterial genome folding	40

Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	40
Machine learning approaches in predicting allosteric sites	40
Navigating the complexities of multi-domain protein folding	40
Template matching and machine learning for cryo-electron tomography	39
Editorial Board	39
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	39
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	39
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	39
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	38
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	38
Structural basis of mRNA maturation: Time to put it together	38
Editorial overview: Protein-nucleic acid interactions: From origins to design	38
Structure-based approaches in synthetic lethality strategies	38
Cryo-EM: A window into the dynamic world of RNA molecules	37
High-speed atomic force microscopy of membrane and membrane protein dynamics	37
In-cell chromatin structure by Cryo-FIB and Cryo-ET	37
Nexus between RNA conformational dynamics and functional versatility	37
Decrypting cryptic pockets with physics-based simulations and artificial intelligence	36
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	36
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	36
Teaching AI to speak protein	36
Applications and prospects of cryo-electron tomography in drug discovery and understanding disease	35
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	34
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	33
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	33
Table of contents	33
Editorial Board	33
The conformationally dynamic structural biology of lanthipeptide biosynthesis	32
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	32
Absolute quantification of protein number and dynamics in single cells	32
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	32
Editorial overview: 3D Genome Chromatin organization and regulation	32
Editorial overview - New Concepts in Drug Discovery (2025)	32
Protein structure prediction in the deep learning era	31
Large-scale protein clustering in the age of deep learning	31
Interpreting chemical crosslinks: Score-based approaches and deep neural networks	31
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	31
Automated pipelines for rapid evaluation during cryoEM data acquisition	31
The material properties of mitotic chromosomes	31
Lipid scrambling: New players, new questions, new opportunities	31
The evolving role of single-molecule force spectroscopy in protein biophysics	30
Application of message passing neural networks for molecular property prediction	30
Recent advances in machine learning predictions of protein-ligand binding affinities	30
Single-molecule fluorescence spectroscopy of fast protein dynamics	30
Commonly asked questions about transcriptional activation domains	29
Application of AI in biological age prediction	29
Multiscale biomolecular simulations in the exascale era	29
Editorial Board	29
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	29
Editorial overview: Folding and Binding (2024)	29
Apprehensions and emerging solutions in ML-based protein structure prediction	28
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	28
Organization of transcription and 3D genome as revealed by live-cell imaging	28
Recent advances and current trends in cryo-electron microscopy	27
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	27
Structural biology of γδ T cell receptors	27
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	27
Advances and applications of microcrystal electron diffraction (MicroED)	27
Metabolic disruptions through a three-dimensional genomic lens	27
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	26
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	26
Modeling flexible RNA 3D structures and RNA-protein complexes	26
Industrializing AI/ML during the end-to-end drug discovery process	25
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	25
Recent advances in AI-driven protein-ligand interaction predictions	25
Exascale simulations and beyond	25
Generative artificial intelligence for de novo protein design	25
Minimal models for RNA simulations	25
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	24
All-atom virus simulations to tackle airborne disease	24
Databases and web-based tools for studying structures of protein-nucleic acid complexes	24
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	24
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	24
Mechanical forces and the 3D genome	24
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	24
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	23
Innovations in targeting RNA by fragment-based ligand discovery	23
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	23
Graphene in cryo-EM specimen optimization	23
β-barrel membrane proteins fold via hybrid-barrel intermediate states	23

Sugar rush: Structural breakdown of plant sugar transport	23
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	23
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	23
AlphaFold2 protein structure prediction: Implications for drug discovery	23
Cryo-EM of the injectisome and type III secretion systems	22
Future prospects for human genetics and genomics in drug discovery	22
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	22
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	22
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	22
Global dynamics behind enzyme catalysis, evolution, and design	22
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	22
Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges	22
Table of contents	22
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery	22
Conformational inhibitors of protein aggregation	21
Base excision repair hierarchy in eukaryotes: Intrinsically disordered region-mediated regulation of genomic surveillance and assembly dynamics	21
AI for targeted polypharmacology: The next frontier in drug discovery	21
Repair and tolerance of DNA damage at the replication fork: A structural perspective	21
Making the cut: Multiscale simulation of membrane remodeling	21
Helical reconstruction, again	21
Protein dynamics by the combination of high-speed AFM and computational modeling	21
Table of contents	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Recent advances in modeling and simulation of biological phenomena in crowded and cellular environments	21
A structural perspective on enzymes and their catalytic mechanisms	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Editorial Board	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	20
Salipro technology in membrane protein research	20
Deep learning–based postprocessing and model building for cryo-electron microscopy maps	20
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	20
Telomeric chromatin structure	20
How residence time works in allosteric drugs	20
Chromosome and protein folding: In search for unified principles	20
Editorial Board	20
Mechanism of primer synthesis by Primase-Polymerases	20
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	19
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	19
Diversity of structure and function in Cullin E3 ligases	19
De novo enzyme design: Controlling structure to design function	19
Recent advances in integrative cryoEM/ET toward visualizing the molecular sociology of cellular organelles	19
Transformers as a substrate for structural biology	19
Dynamic Protein-RNA recognition in primary MicroRNA processing	19
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	19
Computational microbiology: Where is artificial intelligence addressing the barriers to large-scale simulations of bacterial cell envelopes?	19
From statistics to deep learning in single-molecule fluorescence resonance energy transfer analysis	18
Chromatin higher-order folding as influenced by preferred values of linker DNA	18
Amyloid fibril polymorphism: Structural mechanisms of assembly and the links to disease	18
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	18
Time resolved applications for Cryo-EM; approaches, challenges and future directions	18
Computer-aided structural modeling and drug discovery for G-protein-coupled receptors in the age of artificial intelligence	18
Mapping the binding sites of challenging drug targets	18
Combination of single-molecule Förster resonance energy transfer and hydrogen-deuterium exchange mass spectrometry toward dynamic structural biology	18
Editorial overview: New concept in drug discovery	18
Structural studies of the spliceosome: Bridging the gaps	18
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	17
Exploring protein conformations in vitro and in cell with EPR distance measurements	17
Table of contents	17
Diverse modes of regulating methyltransferase activity by histone ubiquitination	17
Structure and function of histone chaperones in replication-coupled chromatin assembly	17
Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates?	17
Artificial intelligence for compound pharmacokinetics prediction	17
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	17
From sequence to structure: A comprehensive review of deep learning models for RNA structure prediction	17
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	17
Allosteric communication and signal transduction in proteins	17
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	17
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	17
Cool and collected: Advances in sample preparation for cryo-electron microscopy	16
Modern machine learning methods for protein property prediction	16
Editorial Board	16
Modern approaches to improving phase contrast electron microscopy	16
Multiscale models of integrins and cellular adhesions	16
Table of contents	16
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	16
Drug–target residence time: Analyzing cooperativity effects in G protein-coupled receptors by mathematical modeling and molecular dynamics simulations	16
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	16
Artificial intelligence in molecular de novo design: Integration with experiment	16
Progress at protein structure prediction, as seen in CASP15	16
Structural biology of SARS-CoV-2 Mpro and drug discovery	15
Characterizing heterogeneity in amyloid formation processes	15
Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy	15
Allostery, engineering and inhibition of tryptophan synthase	15
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	15
Artificial intelligence methods for protein folding and design	15
3D genome organization and beyond!	15
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins	15
Protein ligand structure prediction: From empirical to deep learning approaches	15
Recent advances in DNA-encoded libraries: From covalent targeting to protein profiling	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
Structural highlights of macromolecular complexes and assemblies	15
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	15
Protein-nucleic acid complexes: Docking and binding affinity	15
Editorial overview	15
From snapshots to ensembles: Integrating experimental data and dynamics	15