Current Opinion in Structural Biology

Article	Citations
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	174
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	165
Raman spectroscopy and imaging of protein droplet formation and aggregation	128
How molecular modelling can better broaden the understanding of glycosylations	127
Mutational fitness landscape and drug resistance	124
Editorial	123
Harnessing the 14-3-3 protein–protein interaction network	118
May the proton motive force be with you: A plant transporter review	108
Catalysis and structure of nitrogenases	99
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	93
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	88
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	88
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	83
Computer-aided drug design, quantum-mechanical methods for biological problems	81
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	79
Genome modeling: From chromatin fibers to genes	77
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	76
NMR tools to detect protein allostery	75
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	71
Implications of disease-related mutations at protein–protein interfaces	71
Conformational penalties: New insights into nucleic acid recognition	71
Modeling membranes in situ	70
Markov field models: Scaling molecular kinetics approaches to large molecular machines	67
Advancing protein structure prediction beyond AlphaFold2	66
Dynamics and interactions of intrinsically disordered proteins	65

Structural insights into host–microbe glycointeractions	65
Editorial Board	65
Molecular dynamics simulations for the study of chromatin biology	62
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	62
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	59
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	57
Mucin networks: Dynamic structural assemblies controlling mucus function	57
Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	56
Protein dynamics underlying allosteric regulation	56
The mannose receptor ligands and the macrophage glycome	53
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	52
Principles of nucleosome recognition by chromatin factors and enzymes	52
Inner workings of RAG recombinase and its specialization for adaptive immunity	52
Table of contents	51
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	50
Editorial Board	50
Macromolecular assemblies: Molecular mechanisms abound	50
Table of contents	50
The role of RNA structure in 3’ end processing in eukaryotes	48
Structural insights into assembly of transcription preinitiation complex	47
Challenges and compromises: Predicting unbound antibody structures with deep learning	45
Probing protein–DNA interactions and compaction in nanochannels	45
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	44
Photo-crosslinkers boost structural information from crosslinking mass spectrometry	43
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	42
DDK promotes DNA replication initiation: Mechanistic and structural insights	42
Microsecond time-resolved cryo-electron microscopy	42
Biomolecular simulations at the exascale: From drug design to organelles and beyond	41
Dynamic interactions drive early spliceosome assembly	41
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	41
Structural host immune-microbiota interactions	40
Viral amyloids: New opportunities for antiviral therapeutic strategies	40
NMR of RNA - Structure and interactions	40
Computational approaches to predict protein functional families and functional sites	40
Cryo-EM diversifies	39
Table of contents	39
Insights in bacterial genome folding	39
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	38
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	38
The CMG DNA helicase and the core replisome	38
Integrating cellular and molecular structures and dynamics into whole-cell models	38
Nuclear periphery and its mechanical regulation in cell fate transitions	37
Engineering Cas9 for human genome editing	37
Are N-linked glycans intrinsically disordered?	36
Template matching and machine learning for cryo-electron tomography	36
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	35
Navigating the complexities of multi-domain protein folding	35
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	34
Machine learning approaches in predicting allosteric sites	34
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	34

Structural biology in the age of X-ray free-electron lasers and exascale computing	34
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	33
Nexus between RNA conformational dynamics and functional versatility	33
New insights into Raf regulation from structural analyses	33
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	33
Post-translational modification of RAS proteins	33
Editorial Board	33
Teaching AI to speak protein	33
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	32
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	32
Modeling biomolecular kinetics with large-scale simulation	32
CRISPR/Cas9-based directed evolution in mammalian cells	32
Measuring change in glycoprotein structure	31
Structure-based approaches in synthetic lethality strategies	31
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	30
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	30
Cryo-EM: A window into the dynamic world of RNA molecules	30
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	29
Mass spectrometry informs the structure and dynamics of membrane proteins involved in lipid and drug transport	29
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	29
In-cell chromatin structure by Cryo-FIB and Cryo-ET	29
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	29
Editorial Board	28
Editorial overview: 3D Genome Chromatin organization and regulation	28
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	28
Table of contents	28
Structural basis of mRNA maturation: Time to put it together	28
Interplay among transacting factors around promoter in the initial phases of transcription	27
Toward the equilibrium and kinetics of amyloid peptide self-assembly	27
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	27
Membrane proteins enter the fold	27
Deep learning methods for 3D structural proteome and interactome modeling	27
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	27
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	26
Editorial overview - New Concepts in Drug Discovery (2025)	26
Absolute quantification of protein number and dynamics in single cells	26
The conformationally dynamic structural biology of lanthipeptide biosynthesis	26
Automated pipelines for rapid evaluation during cryoEM data acquisition	26
Protein structure prediction in the deep learning era	26
Techniques for studying membrane pores	26
Commonly asked questions about transcriptional activation domains	26
Application of AI in biological age prediction	26
The material properties of mitotic chromosomes	26
Multiscale biomolecular simulations in the exascale era	25
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	25
Advances and applications of microcrystal electron diffraction (MicroED)	25
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	25
Editorial overview: Folding and Binding (2024)	25
Application of message passing neural networks for molecular property prediction	25
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	25
Adaptive machine learning for protein engineering	25
How much can physics do for protein design?	25
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	24
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	24
Recent advances in AI-driven protein-ligand interaction predictions	24
Organization of transcription and 3D genome as revealed by live-cell imaging	24
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	24
Apprehensions and emerging solutions in ML-based protein structure prediction	24
Recent advances and current trends in cryo-electron microscopy	24
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	24
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	24
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	24
Editorial overview: Catalysis and regulation: The beating heart of biology	24
Cryo-EM of the injectisome and type III secretion systems	23
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	23
Recent developments in multiscale free energy simulations	23
All-atom virus simulations to tackle airborne disease	23
Minimal models for RNA simulations	23
Generative artificial intelligence for de novo protein design	23
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	23
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	23
β-barrel membrane proteins fold via hybrid-barrel intermediate states	23
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems	23
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	23
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	23
Industrializing AI/ML during the end-to-end drug discovery process	23
Innovations in targeting RNA by fragment-based ligand discovery	23
Future prospects for human genetics and genomics in drug discovery	22
Exascale simulations and beyond	22
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	22

Table of contents	22
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	22
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries	22
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	22
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	22
Table of contents	22
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	22
Graphene in cryo-EM specimen optimization	22
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes	22
Mechanical forces and the 3D genome	22
AlphaFold2 protein structure prediction: Implications for drug discovery	22
A structural perspective on enzymes and their catalytic mechanisms	22
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	22
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
Emerging structure-based computational methods to screen the exploding accessible chemical space	21
Conformational inhibitors of protein aggregation	21
Making the cut: Multiscale simulation of membrane remodeling	21
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	21
Structural enzymology of cholesterol biosynthesis and storage	21
Neutron crystallography for the elucidation of enzyme catalysis	21
Protein dynamics by the combination of high-speed AFM and computational modeling	21
AI for targeted polypharmacology: The next frontier in drug discovery	21
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	20
Helical reconstruction, again	20
Editorial Board	20
Time resolved applications for Cryo-EM; approaches, challenges and future directions	20
Table of contents	20
Telomeric chromatin structure	19
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	19
Toward better drug discovery with knowledge graph	19
Editorial Board	19
Salipro technology in membrane protein research	19
Mechanism of primer synthesis by Primase-Polymerases	19
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	18
Protein-based molecular recognition tools for detecting and profiling RNA modifications	18
Allosteric communication and signal transduction in proteins	18
Chromosome and protein folding: In search for unified principles	18
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	18
Diversity of structure and function in Cullin E3 ligases	18
Editorial Board	18
Multiscale models of integrins and cellular adhesions	18
Gas-phase infrared spectroscopy of glycans and glycoconjugates	18
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	18
Unraveling linker histone interactions in nucleosomes	18
Dynamic Protein-RNA recognition in primary MicroRNA processing	18
Editorial overview: New concept in drug discovery	18
Table of contents	18
Structure and function of histone chaperones in replication-coupled chromatin assembly	18
Mapping the binding sites of challenging drug targets	18
Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy	18
Structural studies of the spliceosome: Bridging the gaps	18
Diverse modes of regulating methyltransferase activity by histone ubiquitination	17
Innovations in cryo-electron tomography for tissues: Challenges and future prospects	17
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	17
Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases	17
Artificial intelligence for compound pharmacokinetics prediction	17
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	17
Progress at protein structure prediction, as seen in CASP15	17
Modern approaches to improving phase contrast electron microscopy	17
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	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
Artificial intelligence in molecular de novo design: Integration with experiment	17
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	17
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	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
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	17
Exploring protein conformations in vitro and in cell with EPR distance measurements	17
Table of contents	16
Awakening of the zygotic genome by pioneer transcription factors	16
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	16
New classes of E3 ligases illuminated by chemical probes	16
Dynamic equilibria in protein kinases	16
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	16
Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
Protein-nucleic acid complexes: Docking and binding affinity	15
Structural highlights of macromolecular complexes and assemblies	15
Towards an atomic model of a beating ciliary axoneme	15
Artificial intelligence methods for protein folding and design	15
Allostery, engineering and inhibition of tryptophan synthase	15
Unifying coarse-grained force fields for folded and disordered proteins	15
Quantitative analysis methods for free diffusion single-molecule FRET experiments	15
Protein ligand structure prediction: From empirical to deep learning approaches	15
Uncovering post-translational modification-associated protein–protein interactions	15
Structural biology of SARS-CoV-2 Mpro and drug discovery	15
3D genome organization and beyond!	15
Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy	15
Characterizing heterogeneity in amyloid formation processes	14
Artificial intelligence challenges for predicting the impact of mutations on protein stability	14
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis	14
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	14
The confluence of machine learning and multiscale simulations	14
Biological insights from integrative modeling of intrinsically disordered protein systems	14