Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	251
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	170
Editorial	144
Next-generation predictors of protein phase behavior	132
Optogenetic enzymes: A deep dive into design and impact	102
Genome modeling: From chromatin fibers to genes	99
Computer-aided drug design, quantum-mechanical methods for biological problems	98
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	96
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	94
Mutational fitness landscape and drug resistance	93
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	88
May the proton motive force be with you: A plant transporter review	86
Catalysis and structure of nitrogenases	85
Recent advances in AI-driven pKa prediction for proteins and small molecules	82
Harnessing the 14-3-3 protein–protein interaction network	82
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	78
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	71
Raman spectroscopy and imaging of protein droplet formation and aggregation	71
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	70
Editorial Board	67
Navigating protein–nucleic acid sequence-structure landscapes with deep learning	67
Markov field models: Scaling molecular kinetics approaches to large molecular machines	67
The mannose receptor ligands and the macrophage glycome	64
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	62
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	61

Advances in native cell membrane nanoparticles system	61
Molecular dynamics simulations for the study of chromatin biology	61
Advancing protein structure prediction beyond AlphaFold2	61
Protein dynamics underlying allosteric regulation	60
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	58
Mucin networks: Dynamic structural assemblies controlling mucus function	57
NMR tools to detect protein allostery	57
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	57
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages	56
Dynamics and interactions of intrinsically disordered proteins	56
The role of RNA structure in 3’ end processing in eukaryotes	55
Modeling membranes in situ	55
DDK promotes DNA replication initiation: Mechanistic and structural insights	55
Conformational penalties: New insights into nucleic acid recognition	55
Table of contents	51
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	51
Table of contents	51
Macromolecular assemblies: Molecular mechanisms abound	50
Probing protein–DNA interactions and compaction in nanochannels	48
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	46
Viral amyloids: New opportunities for antiviral therapeutic strategies	46
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	46
NMR of RNA - Structure and interactions	46
Structural insights into assembly of transcription preinitiation complex	45
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	45
Challenges and compromises: Predicting unbound antibody structures with deep learning	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
Dynamic interactions drive early spliceosome assembly	43
Microsecond time-resolved cryo-electron microscopy	42
Table of contents	42
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	42
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	41
Nuclear periphery and its mechanical regulation in cell fate transitions	41
Structural host immune-microbiota interactions	41
Ligand-like lipid interactions with membrane proteins: Simulations and machine learning	41
Insights in bacterial genome folding	41
Cryo-EM diversifies	41
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	40
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	40
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	40
Solid-state NMR of membrane proteins in situ	39
Navigating the complexities of multi-domain protein folding	39
The CMG DNA helicase and the core replisome	39
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	38
Are N-linked glycans intrinsically disordered?	38
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	38
Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	38
Structural biology in the age of X-ray free-electron lasers and exascale computing	38
Template matching and machine learning for cryo-electron tomography	38

Integrating cellular and molecular structures and dynamics into whole-cell models	38
Editorial overview: Protein-nucleic acid interactions: From origins to design	37
Structure-based approaches in synthetic lethality strategies	37
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	37
In-cell chromatin structure by Cryo-FIB and Cryo-ET	37
Decrypting cryptic pockets with physics-based simulations and artificial intelligence	37
Frustration, dynamics, and catalysis	37
Machine learning approaches in predicting allosteric sites	37
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	37
Nexus between RNA conformational dynamics and functional versatility	36
Measuring change in glycoprotein structure	36
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	35
Editorial Board	35
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	35
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	35
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	35
Structural basis of mRNA maturation: Time to put it together	34
Cryo-EM: A window into the dynamic world of RNA molecules	34
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	34
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	33
Editorial overview: 3D Genome Chromatin organization and regulation	33
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	33
Table of contents	33
Teaching AI to speak protein	33
Absolute quantification of protein number and dynamics in single cells	32
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	32
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	32
Interpreting chemical crosslinks: Score-based approaches and deep neural networks	32
Editorial Board	32
Automated pipelines for rapid evaluation during cryoEM data acquisition	31
The conformationally dynamic structural biology of lanthipeptide biosynthesis	31
The material properties of mitotic chromosomes	30
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	30
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	30
Protein structure prediction in the deep learning era	30
Multiscale biomolecular simulations in the exascale era	30
Large-scale protein clustering in the age of deep learning	30
Lipid scrambling: New players, new questions, new opportunities	30
Application of message passing neural networks for molecular property prediction	29
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	29
Commonly asked questions about transcriptional activation domains	29
Editorial overview - New Concepts in Drug Discovery (2025)	28
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	28
Recent advances in machine learning predictions of protein-ligand binding affinities	28
Application of AI in biological age prediction	28
Advances and applications of microcrystal electron diffraction (MicroED)	27
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	27
Editorial Board	27
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	27
Editorial overview: Folding and Binding (2024)	27
Apprehensions and emerging solutions in ML-based protein structure prediction	27
Modeling flexible RNA 3D structures and RNA-protein complexes	26
Recent advances and current trends in cryo-electron microscopy	26
Recent advances in AI-driven protein-ligand interaction predictions	26
Generative artificial intelligence for de novo protein design	26
Organization of transcription and 3D genome as revealed by live-cell imaging	26
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	26
Structural biology of γδ T cell receptors	26
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	25
β-barrel membrane proteins fold via hybrid-barrel intermediate states	25
Exascale simulations and beyond	25
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	25
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	24
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	24
All-atom virus simulations to tackle airborne disease	24
Cryo-EM of the injectisome and type III secretion systems	24
Graphene in cryo-EM specimen optimization	24
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	24
Innovations in targeting RNA by fragment-based ligand discovery	24
Mechanical forces and the 3D genome	24
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	24
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	24
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	23
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	23
Industrializing AI/ML during the end-to-end drug discovery process	23
Minimal models for RNA simulations	23
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	23
Databases and web-based tools for studying structures of protein-nucleic acid complexes	23
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	23
Future prospects for human genetics and genomics in drug discovery	23

Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	23
Making the cut: Multiscale simulation of membrane remodeling	22
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	22
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	22
Table of contents	22
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	22
AlphaFold2 protein structure prediction: Implications for drug discovery	22
Global dynamics behind enzyme catalysis, evolution, and design	21
Conformational inhibitors of protein aggregation	21
Structural enzymology of cholesterol biosynthesis and storage	21
A structural perspective on enzymes and their catalytic mechanisms	21
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery	21
Table of contents	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Helical reconstruction, again	21
Repair and tolerance of DNA damage at the replication fork: A structural perspective	21
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Protein dynamics by the combination of high-speed AFM and computational modeling	21
AI for targeted polypharmacology: The next frontier in drug discovery	20
Deep learning–based postprocessing and model building for cryo-electron microscopy maps	20
Editorial Board	20
Editorial Board	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	20
Table of contents	20
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	20
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	20
Chromosome and protein folding: In search for unified principles	20
Salipro technology in membrane protein research	19
Mapping the binding sites of challenging drug targets	19
Transformers as a substrate for structural biology	19
Telomeric chromatin structure	19
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	19
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	19
Mechanism of primer synthesis by Primase-Polymerases	19
Diversity of structure and function in Cullin E3 ligases	19
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	19
How residence time works in allosteric drugs	19
Dynamic Protein-RNA recognition in primary MicroRNA processing	19
Time resolved applications for Cryo-EM; approaches, challenges and future directions	19
Structural studies of the spliceosome: Bridging the gaps	18
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	18
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	18
Editorial overview: New concept in drug discovery	18
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	18
Modern approaches to improving phase contrast electron microscopy	18
Chromatin higher-order folding as influenced by preferred values of linker DNA	18
Progress at protein structure prediction, as seen in CASP15	18
Modern machine learning methods for protein property prediction	18
Artificial intelligence for compound pharmacokinetics prediction	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
Drug–target residence time: Analyzing cooperativity effects in G protein-coupled receptors by mathematical modeling and molecular dynamics simulations	17
Multiscale models of integrins and cellular adhesions	17
Cool and collected: Advances in sample preparation for cryo-electron microscopy	17
Table of contents	17
Structure and function of histone chaperones in replication-coupled chromatin assembly	17
Allosteric communication and signal transduction in proteins	17
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	17
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	17
Uncovering post-translational modification-associated protein–protein interactions	16
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	16
Diverse modes of regulating methyltransferase activity by histone ubiquitination	16
From sequence to structure: A comprehensive review of deep learning models for RNA structure prediction	16
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	16
Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy	16
Allostery, engineering and inhibition of tryptophan synthase	16
Exploring protein conformations in vitro and in cell with EPR distance measurements	16
Artificial intelligence in molecular de novo design: Integration with experiment	16
Editorial overview	16
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	16
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	16
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	16
Artificial intelligence methods for protein folding and design	15
Structural biology of SARS-CoV-2 Mpro and drug discovery	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
Protein ligand structure prediction: From empirical to deep learning approaches	15
Protein-nucleic acid complexes: Docking and binding affinity	15
Table of contents	15
Editorial Board	15
Integrative modelling of biomolecular dynamics	14
3D genome organization and beyond!	14
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins	14
Quantitative analysis methods for free diffusion single-molecule FRET experiments	14
Molecular models of bidirectional promoter regulation	14
The confluence of machine learning and multiscale simulations	14
From snapshots to ensembles: Integrating experimental data and dynamics	14
In situ structural studies of membrane protein megacomplexes	14
Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy	14
Recent advances and future trends for protein–small molecule interaction predictions with protein language models	14
Structural highlights of macromolecular complexes and assemblies	14
Characterizing heterogeneity in amyloid formation processes	14
Towards an atomic model of a beating ciliary axoneme	14
Biological insights from integrative modeling of intrinsically disordered protein systems	14
Catalysis by Nature's photoenzymes	14