Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	192
Editorial	187
Raman spectroscopy and imaging of protein droplet formation and aggregation	141
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	137
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	131
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	116
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	110
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	101
Genome modeling: From chromatin fibers to genes	100
Catalysis and structure of nitrogenases	98
Harnessing the 14-3-3 protein–protein interaction network	84
May the proton motive force be with you: A plant transporter review	84
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	84
Computer-aided drug design, quantum-mechanical methods for biological problems	83
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	83
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	78
Optogenetic enzymes: A deep dive into design and impact	78
Editorial Board	77
Mutational fitness landscape and drug resistance	77
Protein dynamics underlying allosteric regulation	76
Mucin networks: Dynamic structural assemblies controlling mucus function	75
NMR tools to detect protein allostery	74
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	71
Molecular dynamics simulations for the study of chromatin biology	71
Structural insights into host–microbe glycointeractions	70

Inner workings of RAG recombinase and its specialization for adaptive immunity	65
Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	63
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	61
Advances in native cell membrane nanoparticles system	59
Modeling membranes in situ	59
Dynamics and interactions of intrinsically disordered proteins	59
The mannose receptor ligands and the macrophage glycome	58
Markov field models: Scaling molecular kinetics approaches to large molecular machines	56
Advancing protein structure prediction beyond AlphaFold2	56
Implications of disease-related mutations at protein–protein interfaces	54
Principles of nucleosome recognition by chromatin factors and enzymes	52
Conformational penalties: New insights into nucleic acid recognition	52
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	52
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	49
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	48
Probing protein–DNA interactions and compaction in nanochannels	47
Challenges and compromises: Predicting unbound antibody structures with deep learning	46
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	44
Biomolecular simulations at the exascale: From drug design to organelles and beyond	44
Artificial intelligence in therapeutic antibody design: Advances and future prospects	44
The role of RNA structure in 3’ end processing in eukaryotes	44
Microsecond time-resolved cryo-electron microscopy	44
Table of contents	43
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	43
Table of contents	43
DDK promotes DNA replication initiation: Mechanistic and structural insights	42
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	42
Macromolecular assemblies: Molecular mechanisms abound	42
Viral amyloids: New opportunities for antiviral therapeutic strategies	42
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	41
Structural insights into assembly of transcription preinitiation complex	41
Dynamic interactions drive early spliceosome assembly	41
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	41
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	41
NMR of RNA - Structure and interactions	40
Table of contents	39
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	39
Integrating cellular and molecular structures and dynamics into whole-cell models	39
Navigating the complexities of multi-domain protein folding	39
Nuclear periphery and its mechanical regulation in cell fate transitions	38
Frustration, dynamics, and catalysis	38
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	38
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	38
Are N-linked glycans intrinsically disordered?	38
Template matching and machine learning for cryo-electron tomography	38
Insights in bacterial genome folding	37
Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	37
Cryo-EM diversifies	36
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	36
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	35

Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	35
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	35
Structural host immune-microbiota interactions	35
Machine learning approaches in predicting allosteric sites	34
Solid-state NMR of membrane proteins in situ	34
Structural biology in the age of X-ray free-electron lasers and exascale computing	34
The CMG DNA helicase and the core replisome	34
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	33
Nexus between RNA conformational dynamics and functional versatility	33
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	32
In-cell chromatin structure by Cryo-FIB and Cryo-ET	32
Post-translational modification of RAS proteins	32
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	32
Teaching AI to speak protein	31
Cryo-EM: A window into the dynamic world of RNA molecules	31
Modeling biomolecular kinetics with large-scale simulation	31
Structural basis of mRNA maturation: Time to put it together	31
Structure-based approaches in synthetic lethality strategies	31
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	31
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	31
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	31
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	30
Editorial Board	30
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	30
Measuring change in glycoprotein structure	30
New insights into Raf regulation from structural analyses	30
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	29
Editorial overview: 3D Genome Chromatin organization and regulation	29
Table of contents	29
Large-scale protein clustering in the age of deep learning	28
Interplay among transacting factors around promoter in the initial phases of transcription	28
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	28
Editorial overview - New Concepts in Drug Discovery (2025)	28
Commonly asked questions about transcriptional activation domains	28
Absolute quantification of protein number and dynamics in single cells	28
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	28
Automated pipelines for rapid evaluation during cryoEM data acquisition	28
Adaptive machine learning for protein engineering	28
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	28
The conformationally dynamic structural biology of lanthipeptide biosynthesis	28
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	28
Application of AI in biological age prediction	28
Editorial Board	27
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	27
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	27
Deep learning methods for 3D structural proteome and interactome modeling	27
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	27
The material properties of mitotic chromosomes	27
Application of message passing neural networks for molecular property prediction	26
Modeling flexible RNA 3D structures and RNA-protein complexes	26
Recent advances and current trends in cryo-electron microscopy	26
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	26
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	26
Editorial overview: Folding and Binding (2024)	26
Protein structure prediction in the deep learning era	26
Generative artificial intelligence for de novo protein design	26
Apprehensions and emerging solutions in ML-based protein structure prediction	26
Multiscale biomolecular simulations in the exascale era	26
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	26
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	26
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	26
Editorial overview: Catalysis and regulation: The beating heart of biology	25
Exascale simulations and beyond	25
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	25
How much can physics do for protein design?	25
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	25
Recent advances in AI-driven protein-ligand interaction predictions	25
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	25
Organization of transcription and 3D genome as revealed by live-cell imaging	25
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	25
Advances and applications of microcrystal electron diffraction (MicroED)	25
All-atom virus simulations to tackle airborne disease	24
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	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	24
Databases and web-based tools for studying structures of protein-nucleic acid complexes	24
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	24
Innovations in targeting RNA by fragment-based ligand discovery	24
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	24
Graphene in cryo-EM specimen optimization	24

Future prospects for human genetics and genomics in drug discovery	24
Recent developments in multiscale free energy simulations	24
Minimal models for RNA simulations	23
Industrializing AI/ML during the end-to-end drug discovery process	23
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	23
β-barrel membrane proteins fold via hybrid-barrel intermediate states	23
Cryo-EM of the injectisome and type III secretion systems	23
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	23
AlphaFold2 protein structure prediction: Implications for drug discovery	22
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	22
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	22
Mechanical forces and the 3D genome	22
Neutron crystallography for the elucidation of enzyme catalysis	21
Helical reconstruction, again	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Table of contents	21
Protein dynamics by the combination of high-speed AFM and computational modeling	21
Conformational inhibitors of protein aggregation	21
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	21
Structural enzymology of cholesterol biosynthesis and storage	21
Making the cut: Multiscale simulation of membrane remodeling	21
AI for targeted polypharmacology: The next frontier in drug discovery	21
Table of contents	21
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	21
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	21
Repair and tolerance of DNA damage at the replication fork: A structural perspective	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	20
Editorial Board	20
How residence time works in allosteric drugs	20
Global dynamics behind enzyme catalysis, evolution, and design	20
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	20
Editorial Board	20
A structural perspective on enzymes and their catalytic mechanisms	20
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	20
Unraveling linker histone interactions in nucleosomes	20
Salipro technology in membrane protein research	19
Mechanism of primer synthesis by Primase-Polymerases	19
Dynamic Protein-RNA recognition in primary MicroRNA processing	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
Table of contents	19
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	19
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	19
Telomeric chromatin structure	19
Chromosome and protein folding: In search for unified principles	19
Toward better drug discovery with knowledge graph	19
Editorial overview: New concept in drug discovery	18
Gas-phase infrared spectroscopy of glycans and glycoconjugates	18
Structural studies of the spliceosome: Bridging the gaps	18
Structure and function of histone chaperones in replication-coupled chromatin assembly	18
Mapping the binding sites of challenging drug targets	18
Time resolved applications for Cryo-EM; approaches, challenges and future directions	18
Cool and collected: Advances in sample preparation for cryo-electron microscopy	18
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	18
Modern approaches to improving phase contrast electron microscopy	17
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	17
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	17
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	17
Progress at protein structure prediction, as seen in CASP15	17
Modern machine learning methods for protein property prediction	17
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity	17
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	17
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	17
Exploring protein conformations in vitro and in cell with EPR distance measurements	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
Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases	16
Artificial intelligence in molecular de novo design: Integration with experiment	16
Multiscale models of integrins and cellular adhesions	16
Protein-nucleic acid complexes: Docking and binding affinity	16
Diverse modes of regulating methyltransferase activity by histone ubiquitination	16
Table of contents	16
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	16
Artificial intelligence for compound pharmacokinetics prediction	16
Editorial Board	16
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	16
Allosteric communication and signal transduction in proteins	16
Artificial intelligence methods for protein folding and design	15
Awakening of the zygotic genome by pioneer transcription factors	15
Structural biology of SARS-CoV-2 Mpro and drug discovery	15
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	15
Allostery, engineering and inhibition of tryptophan synthase	15
Editorial Board	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
Table of contents	15
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	15
New classes of E3 ligases illuminated by chemical probes	15
Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy	14
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis	14
Recent advances and future trends for protein–small molecule interaction predictions with protein language models	14
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins	14
Characterizing heterogeneity in amyloid formation processes	14
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	14
Molecular models of bidirectional promoter regulation	14
Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology	14