Current Opinion in Structural Biology

Article	Citations
How molecular modelling can better broaden the understanding of glycosylations	256
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design	179
Editorial	147
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	136
Mutational fitness landscape and drug resistance	108
May the proton motive force be with you: A plant transporter review	103
Computer-aided drug design, quantum-mechanical methods for biological problems	100
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	98
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	97
Navigating protein–nucleic acid sequence-structure landscapes with deep learning	96
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	89
Raman spectroscopy and imaging of protein droplet formation and aggregation	88
Genome modeling: From chromatin fibers to genes	86
Harnessing the 14-3-3 protein–protein interaction network	83
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	82
Catalysis and structure of nitrogenases	79
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	76
Optogenetic enzymes: A deep dive into design and impact	74
Recent advances in AI-driven pKa prediction for proteins and small molecules	72
Next-generation predictors of protein phase behavior	70
Editorial Board	69
Markov field models: Scaling molecular kinetics approaches to large molecular machines	68
Advances in native cell membrane nanoparticles system	67
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	65
Conformational penalties: New insights into nucleic acid recognition	65

Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	65
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	64
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	64
The mannose receptor ligands and the macrophage glycome	62
Advancing protein structure prediction beyond AlphaFold2	60
Dynamics and interactions of intrinsically disordered proteins	59
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages	59
Molecular dynamics simulations for the study of chromatin biology	59
NMR tools to detect protein allostery	58
Mucin networks: Dynamic structural assemblies controlling mucus function	57
Protein dynamics underlying allosteric regulation	56
Modeling membranes in situ	56
Table of contents	55
Macromolecular assemblies: Molecular mechanisms abound	54
Table of contents	53
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	53
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	52
Probing protein–DNA interactions and compaction in nanochannels	51
Viral amyloids: New opportunities for antiviral therapeutic strategies	49
Structural insights into assembly of transcription preinitiation complex	49
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	49
Biomolecular simulations at the exascale: From drug design to organelles and beyond	47
Challenges and compromises: Predicting unbound antibody structures with deep learning	47
Artificial intelligence in therapeutic antibody design: Advances and future prospects	47
Therapeutic implications of target residence time	46
Dynamic interactions drive early spliceosome assembly	46
DDK promotes DNA replication initiation: Mechanistic and structural insights	46
In situ single-particle Cryo-EM methods: Principle and applications	44
NMR of RNA - Structure and interactions	44
The role of RNA structure in 3’ end processing in eukaryotes	44
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	44
Microsecond time-resolved cryo-electron microscopy	43
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	43
Table of contents	43
Navigating the complexities of multi-domain protein folding	42
Structural host immune-microbiota interactions	42
Cryo-EM diversifies	42
The CMG DNA helicase and the core replisome	41
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	41
Nuclear periphery and its mechanical regulation in cell fate transitions	41
Entropy, enthalpy, and evolution: Adaptive trade-offs in protein binding thermodynamics	40
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	40
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	40
Structural biology in the age of X-ray free-electron lasers and exascale computing	40
Integrating cellular and molecular structures and dynamics into whole-cell models	40
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	39
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	39
Solid-state NMR of membrane proteins in situ	39
Template matching and machine learning for cryo-electron tomography	39
Machine learning approaches in predicting allosteric sites	39

Are N-linked glycans intrinsically disordered?	39
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	38
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	38
Frustration, dynamics, and catalysis	38
Insights in bacterial genome folding	38
Ligand-like lipid interactions with membrane proteins: Simulations and machine learning	38
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	37
Editorial overview: Protein-nucleic acid interactions: From origins to design	37
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	37
Structure-based approaches in synthetic lethality strategies	37
Editorial Board	37
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	36
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives	36
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	36
Structural basis of mRNA maturation: Time to put it together	36
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	36
Cryo-EM: A window into the dynamic world of RNA molecules	36
Nexus between RNA conformational dynamics and functional versatility	36
Applications and prospects of cryo-electron tomography in drug discovery and understanding disease	35
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	35
Decrypting cryptic pockets with physics-based simulations and artificial intelligence	35
Teaching AI to speak protein	35
Measuring change in glycoprotein structure	35
In-cell chromatin structure by Cryo-FIB and Cryo-ET	34
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	34
Editorial overview: 3D Genome Chromatin organization and regulation	33
Table of contents	33
Editorial Board	33
Automated pipelines for rapid evaluation during cryoEM data acquisition	32
Absolute quantification of protein number and dynamics in single cells	32
Large-scale protein clustering in the age of deep learning	32
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	32
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	31
Commonly asked questions about transcriptional activation domains	31
Protein structure prediction in the deep learning era	31
The evolving role of single-molecule force spectroscopy in protein biophysics	31
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	30
The conformationally dynamic structural biology of lanthipeptide biosynthesis	30
Multiscale biomolecular simulations in the exascale era	30
Application of AI in biological age prediction	30
Application of message passing neural networks for molecular property prediction	29
The material properties of mitotic chromosomes	29
Single-molecule fluorescence spectroscopy of fast protein dynamics	29
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	29
Editorial Board	28
Interpreting chemical crosslinks: Score-based approaches and deep neural networks	28
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy	28
Organization of transcription and 3D genome as revealed by live-cell imaging	28
Recent advances in machine learning predictions of protein-ligand binding affinities	28
Prediction of nucleic acid binding residues in protein sequences: Recent advances and future prospects	28
Editorial overview: Folding and Binding (2024)	28
Lipid scrambling: New players, new questions, new opportunities	28
Editorial overview - New Concepts in Drug Discovery (2025)	28
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	27
Apprehensions and emerging solutions in ML-based protein structure prediction	27
Recent advances in AI-driven protein-ligand interaction predictions	27
Modeling flexible RNA 3D structures and RNA-protein complexes	27
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	27
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	26
Structural biology of γδ T cell receptors	26
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	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
Advances and applications of microcrystal electron diffraction (MicroED)	26
Graphene in cryo-EM specimen optimization	25
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	25
Exascale simulations and beyond	25
Industrializing AI/ML during the end-to-end drug discovery process	25
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	25
Generative artificial intelligence for de novo protein design	25
Future prospects for human genetics and genomics in drug discovery	25
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	25
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	24
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	24
All-atom virus simulations to tackle airborne disease	24
Innovations in targeting RNA by fragment-based ligand discovery	24
Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges	24
Mechanical forces and the 3D genome	23
Minimal models for RNA simulations	23
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	23

The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	23
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	23
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	23
Cryo-EM of the injectisome and type III secretion systems	23
β-barrel membrane proteins fold via hybrid-barrel intermediate states	22
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	22
Table of contents	22
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	22
Databases and web-based tools for studying structures of protein-nucleic acid complexes	22
Table of contents	22
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	22
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	22
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	22
AlphaFold2 protein structure prediction: Implications for drug discovery	22
Protein dynamics by the combination of high-speed AFM and computational modeling	22
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery	21
Conformational inhibitors of protein aggregation	21
A structural perspective on enzymes and their catalytic mechanisms	21
Global dynamics behind enzyme catalysis, evolution, and design	21
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Making the cut: Multiscale simulation of membrane remodeling	21
Structural enzymology of cholesterol biosynthesis and storage	21
Repair and tolerance of DNA damage at the replication fork: A structural perspective	21
De novo enzyme design: Controlling structure to design function	20
Editorial Board	20
Chromosome and protein folding: In search for unified principles	20
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	20
Base excision repair hierarchy in eukaryotes: Intrinsically disordered region-mediated regulation of genomic surveillance and assembly dynamics	20
Helical reconstruction, again	20
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	20
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	20
AI for targeted polypharmacology: The next frontier in drug discovery	20
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	20
Chromatin higher-order folding as influenced by preferred values of linker DNA	20
Computational microbiology: Where is artificial intelligence addressing the barriers to large-scale simulations of bacterial cell envelopes?	19
Deep learning–based postprocessing and model building for cryo-electron microscopy maps	19
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	19
Diversity of structure and function in Cullin E3 ligases	19
Mechanism of primer synthesis by Primase-Polymerases	19
Editorial Board	19
Table of contents	19
From statistics to deep learning in single-molecule fluorescence resonance energy transfer analysis	19
Telomeric chromatin structure	19
Structural studies of the spliceosome: Bridging the gaps	19
Dynamic Protein-RNA recognition in primary MicroRNA processing	19
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	18
How residence time works in allosteric drugs	18
Editorial overview: New concept in drug discovery	18
Time resolved applications for Cryo-EM; approaches, challenges and future directions	18
Recent advances in integrative cryoEM/ET toward visualizing the molecular sociology of cellular organelles	18
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	18
Transformers as a substrate for structural biology	18
Salipro technology in membrane protein research	18
Mapping the binding sites of challenging drug targets	18
Amyloid fibril polymorphism: Structural mechanisms of assembly and the links to disease	17
Multiscale models of integrins and cellular adhesions	17
Exploring protein conformations in vitro and in cell with EPR distance measurements	17
Modern machine learning methods for protein property prediction	17
Diverse modes of regulating methyltransferase activity by histone ubiquitination	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
Table of contents	17
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	17
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	16
Cool and collected: Advances in sample preparation for cryo-electron microscopy	16
Progress at protein structure prediction, as seen in CASP15	16
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	16
Structure and function of histone chaperones in replication-coupled chromatin assembly	16
Allosteric communication and signal transduction in proteins	16
Modern approaches to improving phase contrast electron microscopy	16
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	16
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	16
Computer-aided structural modeling and drug discovery for G-protein-coupled receptors in the age of artificial intelligence	16
Artificial intelligence in molecular de novo design: Integration with experiment	16
From sequence to structure: A comprehensive review of deep learning models for RNA structure prediction	16
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	16
Drug–target residence time: Analyzing cooperativity effects in G protein-coupled receptors by mathematical modeling and molecular dynamics simulations	15
Editorial overview	15
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	15
Artificial intelligence for compound pharmacokinetics prediction	15
Protein-nucleic acid complexes: Docking and binding affinity	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	15
Allostery, engineering and inhibition of tryptophan synthase	15
Towards an atomic model of a beating ciliary axoneme	14
Biological insights from integrative modeling of intrinsically disordered protein systems	14
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	14
Catalysis by Nature's photoenzymes	14
Quantitative analysis methods for free diffusion single-molecule FRET experiments	14
Probing allosteric communication with combined molecular dynamics simulations and network analysis	14
Characterizing heterogeneity in amyloid formation processes	14
In situ structural studies of membrane protein megacomplexes	14
Recent advances and future trends for protein–small molecule interaction predictions with protein language models	14
The confluence of machine learning and multiscale simulations	14