Current Opinion in Structural Biology

Article	Citations
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	160
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	135
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	121
How molecular modelling can better broaden the understanding of glycosylations	112
Mutational fitness landscape and drug resistance	111
Editorial	110
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	101
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	100
Computer-aided drug design, quantum-mechanical methods for biological problems	99
Harnessing the 14-3-3 protein–protein interaction network	88
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	85
May the proton motive force be with you: A plant transporter review	80
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	76
Catalysis and structure of nitrogenases	76
Genome modeling: From chromatin fibers to genes	73
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	71
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	68
Mucin networks: Dynamic structural assemblies controlling mucus function	66
NMR tools to detect protein allostery	66
The mannose receptor ligands and the macrophage glycome	65
Structural insights into host–microbe glycointeractions	65
Modeling membranes in situ	64
Principles of nucleosome recognition by chromatin factors and enzymes	64
Gut power: Modulation of human amyloid formation by amyloidogenic proteins in the gastrointestinal tract	63
Conformational penalties: New insights into nucleic acid recognition	60

Advancing protein structure prediction beyond AlphaFold2	59
Quantitative characterization of O-GalNAc glycosylation	59
Inner workings of RAG recombinase and its specialization for adaptive immunity	59
Editorial Board	59
Markov field models: Scaling molecular kinetics approaches to large molecular machines	56
Implications of disease-related mutations at protein–protein interfaces	54
Protein dynamics underlying allosteric regulation	54
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods	52
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction	51
Molecular dynamics simulations for the study of chromatin biology	51
Dynamics and interactions of intrinsically disordered proteins	50
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles	50
Challenges and compromises: Predicting unbound antibody structures with deep learning	48
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease	48
Structural insights into assembly of transcription preinitiation complex	48
Viral amyloids: New opportunities for antiviral therapeutic strategies	47
Biomolecular simulations at the exascale: From drug design to organelles and beyond	46
Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery	46
CryoEM of V-ATPases: Assembly, disassembly, and inhibition	45
Table of contents	44
Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations	44
Editorial Board	44
Table of contents	44
Macromolecular assemblies: Molecular mechanisms abound	43
Probing protein–DNA interactions and compaction in nanochannels	42
The role of RNA structure in 3’ end processing in eukaryotes	42
Computational approaches to predict protein functional families and functional sites	42
NMR of RNA - Structure and interactions	41
Dynamic interactions drive early spliceosome assembly	41
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors	40
A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data	39
Microsecond time-resolved cryo-electron microscopy	39
DDK promotes DNA replication initiation: Mechanistic and structural insights	39
Table of contents	37
Engineering Cas9 for human genome editing	37
Structural host immune-microbiota interactions	37
Nuclear periphery and its mechanical regulation in cell fate transitions	37
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies	36
Cryo-EM diversifies	36
Integrating cellular and molecular structures and dynamics into whole-cell models	35
The CMG DNA helicase and the core replisome	35
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex	35
Reading the glyco-code: New approaches to studying protein–carbohydrate interactions	35
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)	35
Insights in bacterial genome folding	35
Integrating AI in fighting advancing Alzheimer: diagnosis, prevention, treatment, monitoring, mechanisms, and clinical trials	34
Protein diversification through post-translational modifications, alternative splicing, and gene duplication	34
Editorial Board	34
Navigating the complexities of multi-domain protein folding	34
Structural biology in the age of X-ray free-electron lasers and exascale computing	34

Machine learning approaches in predicting allosteric sites	34
Modeling biomolecular kinetics with large-scale simulation	33
Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins	33
RETRACTED: Liquid-EM goes viral – visualizing structure and dynamics	33
Nexus between RNA conformational dynamics and functional versatility	32
New insights into Raf regulation from structural analyses	32
Teaching AI to speak protein	31
Measuring change in glycoprotein structure	31
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches	30
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications	30
Cryo-EM: A window into the dynamic world of RNA molecules	30
CRISPR/Cas9-based directed evolution in mammalian cells	30
Mass spectrometry informs the structure and dynamics of membrane proteins involved in lipid and drug transport	29
Nucleosomes unwrapped: Structural perspectives on transcription through chromatin	29
Structural basis of mRNA maturation: Time to put it together	29
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments	28
Glycoproteomics: growing up fast	27
ACE2, B0AT1, and SARS-CoV-2 spike protein: Structural and functional implications	27
Structure-based approaches in synthetic lethality strategies	27
Multiscale biomolecular simulations in the exascale era	26
Table of contents	26
Post-translational modification of RAS proteins	26
Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies	26
Editorial Board	26
The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer	26
Editorial overview: 3D Genome Chromatin organization and regulation	26
Membrane proteins enter the fold	25
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases	25
Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases	25
Multiscale simulations of large complexes in conjunction with cryo-EM analysis	25
Absolute quantification of protein number and dynamics in single cells	25
The conformationally dynamic structural biology of lanthipeptide biosynthesis	25
Toward the equilibrium and kinetics of amyloid peptide self-assembly	25
Automated pipelines for rapid evaluation during cryoEM data acquisition	24
Protein structure prediction in the deep learning era	24
Commonly asked questions about transcriptional activation domains	24
Interplay among transacting factors around promoter in the initial phases of transcription	24
Unlocking the secrets of cell boundaries: Exploring assemblies, machineries, and supercomplexes in membranes	24
The material properties of mitotic chromosomes	24
Deep learning methods for 3D structural proteome and interactome modeling	23
Application of AI in biological age prediction	23
Editorial overview: Folding and Binding (2024)	23
Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors	23
Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes	23
Application of message passing neural networks for molecular property prediction	23
Techniques for studying membrane pores	23
Adaptive machine learning for protein engineering	23
Organization of transcription and 3D genome as revealed by live-cell imaging	23
Recent advances and current trends in cryo-electron microscopy	22
Apprehensions and emerging solutions in ML-based protein structure prediction	22
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	22
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	22
Advances and applications of microcrystal electron diffraction (MicroED)	22
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM	22
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	22
Deep learning techniques have significantly impacted protein structure prediction and protein design	22
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	22
Editorial overview: Catalysis and regulation: The beating heart of biology	22
How much can physics do for protein design?	22
Generative artificial intelligence for de novo protein design	22
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	22
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	22
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	22
Exascale simulations and beyond	21
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	21
Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes	21
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	21
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	21
Graphene in cryo-EM specimen optimization	21
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	21
Recent developments in multiscale free energy simulations	21
Mechanical forces and the 3D genome	21
β-barrel membrane proteins fold via hybrid-barrel intermediate states	21
Cryo-EM of the injectisome and type III secretion systems	21
Innovations in targeting RNA by fragment-based ligand discovery	21
Industrializing AI/ML during the end-to-end drug discovery process	20
Table of contents	20
Outer membrane protein evolution	20
Future prospects for human genetics and genomics in drug discovery	20
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy	20

Making the cut: Multiscale simulation of membrane remodeling	20
AlphaFold2 protein structure prediction: Implications for drug discovery	20
Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease	20
Table of contents	20
Structural enzymology of cholesterol biosynthesis and storage	19
Table of contents	19
Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery	19
Neutron crystallography for the elucidation of enzyme catalysis	19
Visualizing RNA structure ensembles by single-molecule correlated chemical probing	19
Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA	19
Helical reconstruction, again	19
Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry	19
AI for targeted polypharmacology: The next frontier in drug discovery	19
Emerging structure-based computational methods to screen the exploding accessible chemical space	19
Protein dynamics by the combination of high-speed AFM and computational modeling	19
Conformational inhibitors of protein aggregation	19
Repair and tolerance of DNA damage at the replication fork: A structural perspective	19
Time resolved applications for Cryo-EM; approaches, challenges and future directions	18
Dynamic Protein-RNA recognition in primary MicroRNA processing	18
Mapping the binding sites of challenging drug targets	18
NleB/SseKs ortholog effectors as a general bacterial monoglycosyltransferase for eukaryotic proteins	18
Editorial Board	18
Editorial overview–Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications	18
Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins	18
Gas-phase infrared spectroscopy of glycans and glycoconjugates	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	17
Toward better drug discovery with knowledge graph	17
Editorial overview: New concept in drug discovery	17
Protein-based molecular recognition tools for detecting and profiling RNA modifications	17
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments	17
Mechanism of primer synthesis by Primase-Polymerases	17
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins	17
Telomeric chromatin structure	17
Editorial Board	17
Multiscale models of integrins and cellular adhesions	17
Recent breakthroughs in computational structural biology harnessing the power of sequences and structures	17
Unraveling linker histone interactions in nucleosomes	17
Structural studies of the spliceosome: Bridging the gaps	17
Diversity of structure and function in Cullin E3 ligases	17
Table of contents	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
Modern machine learning methods for protein property prediction	16
Diverse modes of regulating methyltransferase activity by histone ubiquitination	16
Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design	16
Artificial intelligence for compound pharmacokinetics prediction	16
In silico toxicity studies of traditional Chinese herbal medicine: A mini review	16
Allosteric communication and signal transduction in proteins	16
Modern approaches to improving phase contrast electron microscopy	16
Artificial intelligence in molecular de novo design: Integration with experiment	16
Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases	16
Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins	16
Protein ligand structure prediction: From empirical to deep learning approaches	15
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity	15
Dynamic equilibria in protein kinases	15
Structural dynamics in α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor gating	15
Structural biology of SARS-CoV-2 Mpro and drug discovery	15
Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules	15
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics	15
Progress at protein structure prediction, as seen in CASP15	15
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states	15
Allostery, engineering and inhibition of tryptophan synthase	15
New classes of E3 ligases illuminated by chemical probes	15
Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond	15
Exploring protein conformations in vitro and in cell with EPR distance measurements	15
The host glycomic response to pathogens	15
Table of contents	15
Protein-nucleic acid complexes: Docking and binding affinity	15
Awakening of the zygotic genome by pioneer transcription factors	15
3D genome organization and beyond!	14
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis	14
Unifying coarse-grained force fields for folded and disordered proteins	14
The confluence of machine learning and multiscale simulations	14
Recent advances on the inhibition of human solute carriers: Therapeutic implications and mechanistic insights	14
Uncovering post-translational modification-associated protein–protein interactions	14
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	14
Structural highlights of macromolecular complexes and assemblies	14
Solving the structural puzzle of bacterial glycome	14
Data-driven computational protein design	14
Editorial overview: Protein–carbohydrate complexes and glycosylation	14
Towards an atomic model of a beating ciliary axoneme	14
Molecular models of bidirectional promoter regulation	14
Probing allosteric communication with combined molecular dynamics simulations and network analysis	14
Open data and algorithms for open science in AI-driven molecular informatics	14
Artificial intelligence challenges for predicting the impact of mutations on protein stability	14
Catalysis by Nature's photoenzymes	14
Characterizing heterogeneity in amyloid formation processes	14
Table of contents	13
Design and discovery of metamorphic proteins	13
Deep learning methods for proteome-scale interaction prediction	13
Modelling the assembly and flexibility of antibody structures	13
Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology	13
RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases	13
Decipher enzymes from human microbiota for drug discovery and development	13
Editorial overview: Engineering and design	13