Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	215
Mutational fitness landscape and drug resistance	196
Editorial	147
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	145
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	131
Catalysis and structure of nitrogenases	118
Optogenetic enzymes: A deep dive into design and impact	106
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	106
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	105
Computer-aided drug design, quantum-mechanical methods for biological problems	89
Raman spectroscopy and imaging of protein droplet formation and aggregation	87
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	87
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	86
May the proton motive force be with you: A plant transporter review	85
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	82
Navigating protein–nucleic acid sequence-structure landscapes with deep learning	82
Genome modeling: From chromatin fibers to genes	80
Harnessing the 14-3-3 protein–protein interaction network	79
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	79
Editorial Board	78
Markov field models: Scaling molecular kinetics approaches to large molecular machines	77
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	73
Advancing protein structure prediction beyond AlphaFold2	70
Mucin networks: Dynamic structural assemblies controlling mucus function	68
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	64

Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	64
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	62
Structural insights into host–microbe glycointeractions	62
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	62
Conformational penalties: New insights into nucleic acid recognition	59
Modeling membranes in situ	57
NMR tools to detect protein allostery	57
Implications of disease-related mutations at protein–protein interfaces	56
Advances in native cell membrane nanoparticles system	54
Molecular dynamics simulations for the study of chromatin biology	52
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages	52
Dynamics and interactions of intrinsically disordered proteins	50
The mannose receptor ligands and the macrophage glycome	49
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	48
Protein dynamics underlying allosteric regulation	48
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	48
The role of RNA structure in 3’ end processing in eukaryotes	47
Table of contents	46
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	46
Structural insights into assembly of transcription preinitiation complex	45
Challenges and compromises: Predicting unbound antibody structures with deep learning	45
Macromolecular assemblies: Molecular mechanisms abound	45
Table of contents	45
Artificial intelligence in therapeutic antibody design: Advances and future prospects	44
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	44
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	43
Probing protein–DNA interactions and compaction in nanochannels	43
Viral amyloids: New opportunities for antiviral therapeutic strategies	43
DDK promotes DNA replication initiation: Mechanistic and structural insights	42
NMR of RNA - Structure and interactions	42
Biomolecular simulations at the exascale: From drug design to organelles and beyond	42
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	42
Dynamic interactions drive early spliceosome assembly	42
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	42
Microsecond time-resolved cryo-electron microscopy	42
Nuclear periphery and its mechanical regulation in cell fate transitions	41
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	41
Table of contents	41
Structural biology in the age of X-ray free-electron lasers and exascale computing	40
Machine learning approaches in predicting allosteric sites	40
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	40
Solid-state NMR of membrane proteins in situ	40
Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	39
Cryo-EM diversifies	38
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	38
Structural host immune-microbiota interactions	38
Insights in bacterial genome folding	38
Template matching and machine learning for cryo-electron tomography	37
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	37
Navigating the complexities of multi-domain protein folding	36

Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	36
Are N-linked glycans intrinsically disordered?	36
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	35
In-cell chromatin structure by Cryo-FIB and Cryo-ET	35
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	35
Integrating cellular and molecular structures and dynamics into whole-cell models	35
The CMG DNA helicase and the core replisome	35
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	35
Frustration, dynamics, and catalysis	35
Modeling biomolecular kinetics with large-scale simulation	34
Structure-based approaches in synthetic lethality strategies	34
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	32
Cryo-EM: A window into the dynamic world of RNA molecules	32
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	32
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	32
Editorial Board	32
Nexus between RNA conformational dynamics and functional versatility	32
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	32
Teaching AI to speak protein	32
Measuring change in glycoprotein structure	32
Editorial overview: Protein-nucleic acid interactions: From origins to design	32
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	32
Structural basis of mRNA maturation: Time to put it together	31
Editorial overview: 3D Genome Chromatin organization and regulation	31
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	31
Table of contents	31
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	31
Editorial Board	30
Editorial overview - New Concepts in Drug Discovery (2025)	30
Automated pipelines for rapid evaluation during cryoEM data acquisition	30
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	30
Large-scale protein clustering in the age of deep learning	30
The conformationally dynamic structural biology of lanthipeptide biosynthesis	30
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	30
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	30
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	29
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	29
Protein structure prediction in the deep learning era	29
Absolute quantification of protein number and dynamics in single cells	29
The material properties of mitotic chromosomes	29
Application of AI in biological age prediction	29
Adaptive machine learning for protein engineering	29
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	29
Multiscale biomolecular simulations in the exascale era	28
Application of message passing neural networks for molecular property prediction	28
Commonly asked questions about transcriptional activation domains	28
Deep learning methods for 3D structural proteome and interactome modeling	28
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	28
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	27
How much can physics do for protein design?	27
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	27
Advances and applications of microcrystal electron diffraction (MicroED)	27
Organization of transcription and 3D genome as revealed by live-cell imaging	27
Apprehensions and emerging solutions in ML-based protein structure prediction	27
Editorial overview: Folding and Binding (2024)	27
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	27
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	26
Recent advances and current trends in cryo-electron microscopy	26
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	26
Recent advances in AI-driven protein-ligand interaction predictions	26
Generative artificial intelligence for de novo protein design	26
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	26
Modeling flexible RNA 3D structures and RNA-protein complexes	26
Exascale simulations and beyond	26
β-barrel membrane proteins fold via hybrid-barrel intermediate states	25
All-atom virus simulations to tackle airborne disease	25
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	25
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	25
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	25
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
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	24
Innovations in targeting RNA by fragment-based ligand discovery	24
Cryo-EM of the injectisome and type III secretion systems	24
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	24
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	24
Graphene in cryo-EM specimen optimization	24
Recent developments in multiscale free energy simulations	24
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	23
Databases and web-based tools for studying structures of protein-nucleic acid complexes	23

Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	23
Future prospects for human genetics and genomics in drug discovery	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
Minimal models for RNA simulations	23
AlphaFold2 protein structure prediction: Implications for drug discovery	23
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	23
AI for targeted polypharmacology: The next frontier in drug discovery	22
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	22
Making the cut: Multiscale simulation of membrane remodeling	22
Table of contents	22
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	22
Structural enzymology of cholesterol biosynthesis and storage	22
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	21
Helical reconstruction, again	21
Protein dynamics by the combination of high-speed AFM and computational modeling	21
Editorial Board	21
Table of contents	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Global dynamics behind enzyme catalysis, evolution, and design	21
Repair and tolerance of DNA damage at the replication fork: A structural perspective	21
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery	21
Conformational inhibitors of protein aggregation	21
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	21
A structural perspective on enzymes and their catalytic mechanisms	21
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	21
Editorial Board	20
Dynamic Protein-RNA recognition in primary MicroRNA processing	20
Gas-phase infrared spectroscopy of glycans and glycoconjugates	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	20
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	20
Diversity of structure and function in Cullin E3 ligases	20
Table of contents	20
How residence time works in allosteric drugs	20
Mechanism of primer synthesis by Primase-Polymerases	20
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	19
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	19
Chromatin higher-order folding as influenced by preferred values of linker DNA	19
Toward better drug discovery with knowledge graph	19
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	19
Telomeric chromatin structure	19
Mapping the binding sites of challenging drug targets	19
Chromosome and protein folding: In search for unified principles	19
Structural studies of the spliceosome: Bridging the gaps	18
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	18
Table of contents	18
Salipro technology in membrane protein research	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
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	18
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	18
Editorial overview: New concept in drug discovery	18
Multiscale models of integrins and cellular adhesions	18
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	18
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	17
Structure and function of histone chaperones in replication-coupled chromatin assembly	17
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	17
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	17
Artificial intelligence for compound pharmacokinetics prediction	17
Artificial intelligence in molecular de novo design: Integration with experiment	17
Diverse modes of regulating methyltransferase activity by histone ubiquitination	17
Modern machine learning methods for protein property prediction	17
Allosteric communication and signal transduction in proteins	16
Progress at protein structure prediction, as seen in CASP15	16
Protein ligand structure prediction: From empirical to deep learning approaches	16
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	16
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	16
Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates?	16
Modern approaches to improving phase contrast electron microscopy	16
Exploring protein conformations in vitro and in cell with EPR distance measurements	16
Protein-nucleic acid complexes: Docking and binding affinity	16
New classes of E3 ligases illuminated by chemical probes	15
Editorial Board	15
Editorial overview	15
Recent advances in DNA-encoded libraries: From covalent targeting to protein profiling	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
Artificial intelligence methods for protein folding and design	15
Table of contents	15
From snapshots to ensembles: Integrating experimental data and dynamics	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy	14
Structural highlights of macromolecular complexes and assemblies	14
Biological insights from integrative modeling of intrinsically disordered protein systems	14
Open data and algorithms for open science in AI-driven molecular informatics	14
Structural biology of SARS-CoV-2 Mpro and drug discovery	14
Quantitative analysis methods for free diffusion single-molecule FRET experiments	14
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins	14
Unifying coarse-grained force fields for folded and disordered proteins	14
Recent advances and future trends for protein–small molecule interaction predictions with protein language models	14
Uncovering post-translational modification-associated protein–protein interactions	14
3D genome organization and beyond!	14
Characterizing heterogeneity in amyloid formation processes	14
Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology	14
Molecular models of bidirectional promoter regulation	14