Current Opinion in Structural Biology

Article	Citations
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	168
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	144
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	123
How molecular modelling can better broaden the understanding of glycosylations	119
Mutational fitness landscape and drug resistance	118
Editorial	118
Raman spectroscopy and imaging of protein droplet formation and aggregation	104
Harnessing the 14-3-3 protein–protein interaction network	103
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	102
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	91
Catalysis and structure of nitrogenases	87
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	82
May the proton motive force be with you: A plant transporter review	78
Genome modeling: From chromatin fibers to genes	78
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	75
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	73
Computer-aided drug design, quantum-mechanical methods for biological problems	73
NMR tools to detect protein allostery	70
Quantitative characterization of O-GalNAc glycosylation	69
Conformational penalties: New insights into nucleic acid recognition	67
Advancing protein structure prediction beyond AlphaFold2	66
Editorial Board	65
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	64
Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	64
Inner workings of RAG recombinase and its specialization for adaptive immunity	64

Mucin networks: Dynamic structural assemblies controlling mucus function	62
Structural insights into host–microbe glycointeractions	62
Markov field models: Scaling molecular kinetics approaches to large molecular machines	62
Molecular dynamics simulations for the study of chromatin biology	61
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	58
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	56
Implications of disease-related mutations at protein–protein interfaces	54
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	54
Modeling membranes in situ	54
Protein dynamics underlying allosteric regulation	53
Dynamics and interactions of intrinsically disordered proteins	53
The mannose receptor ligands and the macrophage glycome	52
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	50
Principles of nucleosome recognition by chromatin factors and enzymes	50
Challenges and compromises: Predicting unbound antibody structures with deep learning	49
Viral amyloids: New opportunities for antiviral therapeutic strategies	48
NMR of RNA - Structure and interactions	48
Structural insights into assembly of transcription preinitiation complex	48
Probing protein–DNA interactions and compaction in nanochannels	47
Table of contents	47
Table of contents	46
Editorial Board	46
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	45
Macromolecular assemblies: Molecular mechanisms abound	44
Biomolecular simulations at the exascale: From drug design to organelles and beyond	43
The role of RNA structure in 3’ end processing in eukaryotes	43
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	42
DDK promotes DNA replication initiation: Mechanistic and structural insights	42
Computational approaches to predict protein functional families and functional sites	42
Microsecond time-resolved cryo-electron microscopy	42
Dynamic interactions drive early spliceosome assembly	41
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	41
Structural host immune-microbiota interactions	40
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	40
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	38
Table of contents	38
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	38
Cryo-EM diversifies	38
Engineering Cas9 for human genome editing	37
Structural biology in the age of X-ray free-electron lasers and exascale computing	37
Nuclear periphery and its mechanical regulation in cell fate transitions	37
Insights in bacterial genome folding	37
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	37
Machine learning approaches in predicting allosteric sites	36
Navigating the complexities of multi-domain protein folding	36
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	36
The CMG DNA helicase and the core replisome	36
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	35
Integrating cellular and molecular structures and dynamics into whole-cell models	35
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	34

Modeling biomolecular kinetics with large-scale simulation	34
Editorial Board	34
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	34
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	34
Nexus between RNA conformational dynamics and functional versatility	33
New insights into Raf regulation from structural analyses	32
CRISPR/Cas9-based directed evolution in mammalian cells	32
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	32
Structure-based approaches in synthetic lethality strategies	31
Mass spectrometry informs the structure and dynamics of membrane proteins involved in lipid and drug transport	31
Measuring change in glycoprotein structure	31
Cryo-EM: A window into the dynamic world of RNA molecules	31
Structural basis of mRNA maturation: Time to put it together	31
In-cell chromatin structure by Cryo-FIB and Cryo-ET	30
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	30
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	30
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	30
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	29
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	29
Teaching AI to speak protein	28
Post-translational modification of RAS proteins	28
Glycoproteomics: growing up fast	28
Editorial Board	27
Toward the equilibrium and kinetics of amyloid peptide self-assembly	27
Table of contents	27
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	27
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	27
Editorial overview: 3D Genome Chromatin organization and regulation	27
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	27
Techniques for studying membrane pores	26
Membrane proteins enter the fold	26
Interplay among transacting factors around promoter in the initial phases of transcription	26
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	26
Automated pipelines for rapid evaluation during cryoEM data acquisition	26
Absolute quantification of protein number and dynamics in single cells	26
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	25
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	25
Application of AI in biological age prediction	25
Protein structure prediction in the deep learning era	25
Deep learning methods for 3D structural proteome and interactome modeling	25
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	25
Adaptive machine learning for protein engineering	25
The conformationally dynamic structural biology of lanthipeptide biosynthesis	25
Application of message passing neural networks for molecular property prediction	24
Commonly asked questions about transcriptional activation domains	24
Recent advances in AI-driven protein-ligand interaction predictions	24
Multiscale biomolecular simulations in the exascale era	24
Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes	24
Editorial overview: Folding and Binding (2024)	24
The material properties of mitotic chromosomes	24
Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization	24
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	23
Apprehensions and emerging solutions in ML-based protein structure prediction	23
Deep learning techniques have significantly impacted protein structure prediction and protein design	23
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	23
Advances and applications of microcrystal electron diffraction (MicroED)	23
Generative artificial intelligence for de novo protein design	23
Recent advances and current trends in cryo-electron microscopy	23
Editorial overview: Catalysis and regulation: The beating heart of biology	23
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	23
Organization of transcription and 3D genome as revealed by live-cell imaging	23
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	23
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM	23
How much can physics do for protein design?	23
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	22
Mechanical forces and the 3D genome	22
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	22
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	22
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	22
Future prospects for human genetics and genomics in drug discovery	22
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	22
Exascale simulations and beyond	22
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	22
Recent developments in multiscale free energy simulations	22
β-barrel membrane proteins fold via hybrid-barrel intermediate states	22
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	22
Graphene in cryo-EM specimen optimization	22
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	22
All-atom virus simulations to tackle airborne disease	22
Cryo-EM of the injectisome and type III secretion systems	22

Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	21
Table of contents	21
Neutron crystallography for the elucidation of enzyme catalysis	21
Industrializing AI/ML during the end-to-end drug discovery process	21
Innovations in targeting RNA by fragment-based ligand discovery	21
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	21
Table of contents	21
AlphaFold2 protein structure prediction: Implications for drug discovery	21
Conformational inhibitors of protein aggregation	21
Outer membrane protein evolution	21
A structural perspective on enzymes and their catalytic mechanisms	20
Table of contents	20
Emerging structure-based computational methods to screen the exploding accessible chemical space	20
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	20
Making the cut: Multiscale simulation of membrane remodeling	20
Helical reconstruction, again	20
Structural enzymology of cholesterol biosynthesis and storage	20
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	20
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	20
AI for targeted polypharmacology: The next frontier in drug discovery	20
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	20
Repair and tolerance of DNA damage at the replication fork: A structural perspective	20
Protein dynamics by the combination of high-speed AFM and computational modeling	20
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	19
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	19
Unraveling linker histone interactions in nucleosomes	19
Mapping the binding sites of challenging drug targets	19
Mechanism of primer synthesis by Primase-Polymerases	19
Diversity of structure and function in Cullin E3 ligases	19
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	19
Editorial Board	19
Telomeric chromatin structure	18
Dynamic Protein-RNA recognition in primary MicroRNA processing	18
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins	18
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	18
NleB/SseKs ortholog effectors as a general bacterial monoglycosyltransferase for eukaryotic proteins	18
Toward better drug discovery with knowledge graph	18
Time resolved applications for Cryo-EM; approaches, challenges and future directions	18
Chromosome and protein folding: In search for unified principles	18
Gas-phase infrared spectroscopy of glycans and glycoconjugates	18
Editorial overview: New concept in drug discovery	18
Structural studies of the spliceosome: Bridging the gaps	18
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	17
Protein-based molecular recognition tools for detecting and profiling RNA modifications	17
The host glycomic response to pathogens	17
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	17
Diverse modes of regulating methyltransferase activity by histone ubiquitination	17
Modern approaches to improving phase contrast electron microscopy	17
Editorial Board	17
Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases	17
Structure and function of histone chaperones in replication-coupled chromatin assembly	17
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	17
Artificial intelligence in molecular de novo design: Integration with experiment	17
Table of contents	17
Modern machine learning methods for protein property prediction	17
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	17
Progress at protein structure prediction, as seen in CASP15	17
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	17
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	16
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity	16
Exploring protein conformations in vitro and in cell with EPR distance measurements	16
Allostery, engineering and inhibition of tryptophan synthase	16
Multiscale models of integrins and cellular adhesions	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
Table of contents	16
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	16
Allosteric communication and signal transduction in proteins	16
Artificial intelligence for compound pharmacokinetics prediction	16
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	16
Dynamic equilibria in protein kinases	16
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
3D genome organization and beyond!	15
Characterizing heterogeneity in amyloid formation processes	15
Catalysis by Nature's photoenzymes	15
Awakening of the zygotic genome by pioneer transcription factors	15
Structural biology of SARS-CoV-2 Mpro and drug discovery	15
New classes of E3 ligases illuminated by chemical probes	15
Probing allosteric communication with combined molecular dynamics simulations and network analysis	15
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	15
Protein ligand structure prediction: From empirical to deep learning approaches	15
Uncovering post-translational modification-associated protein–protein interactions	15
Structural highlights of macromolecular complexes and assemblies	15
Molecular models of bidirectional promoter regulation	15
Open data and algorithms for open science in AI-driven molecular informatics	14
Table of contents	14
Editorial overview: Engineering and design	14
Data-driven computational protein design	14
Table of contents	14
Deciphering the dynamic codes: Advances in biomolecular modeling and simulation	14
Structural insights into the recognition of native nucleosomes by pioneer transcription factors	14
The confluence of machine learning and multiscale simulations	14
Editorial overview: Protein–carbohydrate complexes and glycosylation	14
RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases	14
Unifying coarse-grained force fields for folded and disordered proteins	14