Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	201
Mutational fitness landscape and drug resistance	193
Editorial	144
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	142
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	135
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	117
May the proton motive force be with you: A plant transporter review	115
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	104
Optogenetic enzymes: A deep dive into design and impact	103
Raman spectroscopy and imaging of protein droplet formation and aggregation	101
Navigating protein–nucleic acid sequence-structure landscapes with deep learning	86
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	86
Genome modeling: From chromatin fibers to genes	85
Catalysis and structure of nitrogenases	84
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	84
Harnessing the 14-3-3 protein–protein interaction network	82
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	80
Editorial Board	78
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	78
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	78
Computer-aided drug design, quantum-mechanical methods for biological problems	78
Inner workings of RAG recombinase and its specialization for adaptive immunity	77
Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	75
Structural insights into host–microbe glycointeractions	74
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	72

Conformational penalties: New insights into nucleic acid recognition	68
Markov field models: Scaling molecular kinetics approaches to large molecular machines	65
Molecular dynamics simulations for the study of chromatin biology	64
Protein dynamics underlying allosteric regulation	60
NMR tools to detect protein allostery	60
Advancing protein structure prediction beyond AlphaFold2	60
Modeling membranes in situ	60
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages	58
Advances in native cell membrane nanoparticles system	56
Implications of disease-related mutations at protein–protein interfaces	56
The mannose receptor ligands and the macrophage glycome	55
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	53
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	53
Principles of nucleosome recognition by chromatin factors and enzymes	50
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	49
Dynamics and interactions of intrinsically disordered proteins	48
Biomolecular simulations at the exascale: From drug design to organelles and beyond	47
Mucin networks: Dynamic structural assemblies controlling mucus function	47
Challenges and compromises: Predicting unbound antibody structures with deep learning	47
Macromolecular assemblies: Molecular mechanisms abound	46
Table of contents	46
Table of contents	45
Artificial intelligence in therapeutic antibody design: Advances and future prospects	45
Probing protein–DNA interactions and compaction in nanochannels	44
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	44
DDK promotes DNA replication initiation: Mechanistic and structural insights	44
The role of RNA structure in 3’ end processing in eukaryotes	44
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	44
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	44
Microsecond time-resolved cryo-electron microscopy	43
NMR of RNA - Structure and interactions	42
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	42
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	42
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	42
Dynamic interactions drive early spliceosome assembly	42
Table of contents	41
Viral amyloids: New opportunities for antiviral therapeutic strategies	41
Structural insights into assembly of transcription preinitiation complex	41
Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	40
Structural host immune-microbiota interactions	40
Machine learning approaches in predicting allosteric sites	40
Cryo-EM diversifies	40
Integrating cellular and molecular structures and dynamics into whole-cell models	40
Structural biology in the age of X-ray free-electron lasers and exascale computing	40
The CMG DNA helicase and the core replisome	40
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	38
Insights in bacterial genome folding	38
Are N-linked glycans intrinsically disordered?	38
Solid-state NMR of membrane proteins in situ	37
Navigating the complexities of multi-domain protein folding	37

Frustration, dynamics, and catalysis	37
Nuclear periphery and its mechanical regulation in cell fate transitions	37
Template matching and machine learning for cryo-electron tomography	37
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	37
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	36
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	36
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	35
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	35
Nexus between RNA conformational dynamics and functional versatility	35
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	35
Structure-based approaches in synthetic lethality strategies	34
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	34
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	34
In-cell chromatin structure by Cryo-FIB and Cryo-ET	33
Cryo-EM: A window into the dynamic world of RNA molecules	33
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	33
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	33
Post-translational modification of RAS proteins	32
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	32
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	31
Modeling biomolecular kinetics with large-scale simulation	31
New insights into Raf regulation from structural analyses	31
Editorial Board	31
Measuring change in glycoprotein structure	31
Editorial overview - New Concepts in Drug Discovery (2025)	30
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	30
Teaching AI to speak protein	30
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	30
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	30
Structural basis of mRNA maturation: Time to put it together	30
Editorial overview: 3D Genome Chromatin organization and regulation	30
Table of contents	30
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	30
Editorial overview: Protein-nucleic acid interactions: From origins to design	30
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	29
The conformationally dynamic structural biology of lanthipeptide biosynthesis	29
Absolute quantification of protein number and dynamics in single cells	29
Editorial Board	29
Automated pipelines for rapid evaluation during cryoEM data acquisition	28
Adaptive machine learning for protein engineering	28
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	28
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	28
Deep learning methods for 3D structural proteome and interactome modeling	28
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	28
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	28
Multiscale biomolecular simulations in the exascale era	28
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	28
Commonly asked questions about transcriptional activation domains	28
Application of AI in biological age prediction	28
Large-scale protein clustering in the age of deep learning	28
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	28
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	27
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	27
The material properties of mitotic chromosomes	27
Application of message passing neural networks for molecular property prediction	27
Recent advances in AI-driven protein-ligand interaction predictions	27
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	27
Protein structure prediction in the deep learning era	27
Recent advances and current trends in cryo-electron microscopy	27
Apprehensions and emerging solutions in ML-based protein structure prediction	27
Editorial overview: Folding and Binding (2024)	27
Interplay among transacting factors around promoter in the initial phases of transcription	27
Advances and applications of microcrystal electron diffraction (MicroED)	26
Organization of transcription and 3D genome as revealed by live-cell imaging	26
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	26
How much can physics do for protein design?	26
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	26
Generative artificial intelligence for de novo protein design	25
Graphene in cryo-EM specimen optimization	25
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	25
Future prospects for human genetics and genomics in drug discovery	25
Editorial overview: Catalysis and regulation: The beating heart of biology	25
Modeling flexible RNA 3D structures and RNA-protein complexes	25
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	25
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	25
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	25
Exascale simulations and beyond	25
All-atom virus simulations to tackle airborne disease	25
Innovations in targeting RNA by fragment-based ligand discovery	25
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	24

Minimal models for RNA simulations	24
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	24
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	24
Recent developments in multiscale free energy simulations	24
Cryo-EM of the injectisome and type III secretion systems	24
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	24
β-barrel membrane proteins fold via hybrid-barrel intermediate states	23
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	23
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	23
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	23
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	23
Mechanical forces and the 3D genome	23
Databases and web-based tools for studying structures of protein-nucleic acid complexes	23
Industrializing AI/ML during the end-to-end drug discovery process	22
Repair and tolerance of DNA damage at the replication fork: A structural perspective	22
Protein dynamics by the combination of high-speed AFM and computational modeling	22
Table of contents	22
Conformational inhibitors of protein aggregation	22
AlphaFold2 protein structure prediction: Implications for drug discovery	22
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	22
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	22
Table of contents	22
Making the cut: Multiscale simulation of membrane remodeling	22
Global dynamics behind enzyme catalysis, evolution, and design	22
Helical reconstruction, again	22
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	21
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	21
Editorial Board	21
Structural enzymology of cholesterol biosynthesis and storage	21
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery	21
AI for targeted polypharmacology: The next frontier in drug discovery	21
Editorial Board	21
A structural perspective on enzymes and their catalytic mechanisms	21
Neutron crystallography for the elucidation of enzyme catalysis	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	20
Mechanism of primer synthesis by Primase-Polymerases	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	20
Diversity of structure and function in Cullin E3 ligases	20
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	20
Chromosome and protein folding: In search for unified principles	20