Current Opinion in Structural Biology

Article	Citations
Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins	238
Editorial overview: Artificial intelligence (AI) methodologies in structural biology	152
AI-based methods for biomolecular structure modeling for Cryo-EM	127
Protein binding and folding through an evolutionary lens	121
In-cell NMR: From target structure and dynamics to drug screening	120
Single-point mutations in disordered proteins: Linking sequence, ensemble, and function	115
Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions	109
Extending the reach of single-particle cryoEM	107
Foundation models of protein sequences: A brief overview	107
Apprehensions and emerging solutions in ML-based protein structure prediction	98
Artificial intelligence-driven antimicrobial peptide discovery	97
Pump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels	96
Editorial Board	86
Editorial overview: Folding and Binding (2024)	83
Regulation of tau by peptidyl-prolyl isomerases	76
Structural biology and inhibition of the Mtb cell wall glycoconjugates biosynthesis on the membrane	74
Editorial Board	71
HATs meet structural biology	70
Editorial Board	67
Editorial Board	67
3D genome organization and beyond!	66
Editorial Board	65
Organization of transcription and 3D genome as revealed by live-cell imaging	65
Single-cell mapping of cell-type specific chromatin architecture in the central nervous system	64
Advancing biomolecular simulation through exascale HPC, AI and quantum computing	63

Glycosylation as a key parameter in the design of nucleic acid vaccines	61
Molecular models of bidirectional promoter regulation	61
From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor	59
The confluence of machine learning and multiscale simulations	58
Solving the structural puzzle of bacterial glycome	57
Visualizing everything, everywhere, all at once: Cryo-EM and the new field of structureomics	57
RNA helicases are hubs that orchestrate exosome-dependent 3′–5′ decay	57
Structural determinants of regulated proteolysis in pathogenic bacteria by ClpP and the proteasome	57
The role of local versus nonlocal physicochemical restraints in determining protein native structure	56
Structural basis for DNA sequence recognition by pioneer factors in nucleosomes	54
Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers	54
Computational strategies for protein conformational ensemble detection	52
Computer-aided drug design, quantum-mechanical methods for biological problems	52
Combining crystallography with quantum mechanics	51
Multiscale kinetic analysis of proteins	51
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis	50
How much can physics do for protein design?	50
Reweighting methods for elucidation of conformation ensembles of proteins	49
Revealing bacterial cell biology using cryo-electron tomography	48
Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis	47
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins	46
Molecular tools for probing the microbiome	46
Mutational fitness landscape and drug resistance	46
Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases	46
Addressing high excitation conditions in time-resolved X-ray diffraction experiments and issues of biological relevance	45
How molecular modelling can better broaden the understanding of glycosylations	45
In silico reconstitution of DNA replication. Lessons from single-molecule imaging and cryo-tomography applied to single-particle cryo-EM	45
The twisting elevator mechanism of glutamate transporters reveals the structural basis for the dual transport-channel functions	45
The new epoch of structural insights into radical SAM enzymology	44
Bonds and bytes: The odyssey of structural biology	44
PARP–nucleic acid interactions: Allosteric signaling, PARP inhibitor types, DNA bridges, and viral RNA surveillance	44
Harnessing the 14-3-3 protein–protein interaction network	43
Editorial	42
Structural highlights of macromolecular complexes and assemblies	40
Single particle cryo-EM map and model validation: It's not crystal clear	40
Characterizing heterogeneity in amyloid formation processes	40
Transcriptional machinery as an architect of genome structure	40
Context-dependent, fuzzy protein interactions: Towards sequence-based insights	40
Advances and applications of microcrystal electron diffraction (MicroED)	39
Long non-coding RNAs in the nucleolus: Biogenesis, regulation, and function	39
Expansion microscopy: A chemical approach for super-resolution microscopy	38
Editorial overview: Protein networks in health and disease	38
Characterizing protein-protein interactions with thermal proteome profiling	38
Artificial intelligence in the experimental determination and prediction of macromolecular structures	38
Data-driven computational protein design	38
Deep learning techniques have significantly impacted protein structure prediction and protein design	37
The role of intrinsic protein disorder in regulation of cyclin-dependent kinases	36
Untangling the pseudoknots of SARS-CoV-2: Insights into structural heterogeneity and plasticity	35
Artificial intelligence based methods for hot spot prediction	35
Heterotypic amyloid interactions: Clues to polymorphic bias and selective cellular vulnerability?	35

Catalysis by Nature's photoenzymes	35
Genome modeling: From chromatin fibers to genes	35
Recent advances and current trends in cryo-electron microscopy	34
Editorial overview: Catalysis and regulation: The beating heart of biology	34
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM	34
Understanding the structure and function of Plasmodium aminopeptidases to facilitate drug discovery	34
Single-particle Cryo-EM and molecular dynamics simulations: A perfect match	34
Editorial overview: Cryo-electron microscopy	34
Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches	33
Connecting the dots: Computational network analysis for disease insight and drug repurposing	33
May the proton motive force be with you: A plant transporter review	33
Probing allosteric communication with combined molecular dynamics simulations and network analysis	33
Advances in structure-based allosteric drug design	32
Artificial intelligence challenges for predicting the impact of mutations on protein stability	32
Constant pH molecular dynamics simulations: Current status and recent applications	32
Recent progress in general force fields of small molecules	32
Protein structure-based evaluation of missense variants: Resources, challenges and future directions	32
Miniature CRISPR-Cas12 endonucleases – Programmed DNA targeting in a smaller package	31
Structure-based virtual screening of vast chemical space as a starting point for drug discovery	31
Unifying coarse-grained force fields for folded and disordered proteins	31
TADs: Dynamic structures to create stable regulatory functions	31
Federated learning for molecular discovery	29
Open data and algorithms for open science in AI-driven molecular informatics	29
Catalysis and structure of nitrogenases	29
Frontiers in the enzymology of thiamin diphosphate-dependent enzymes	29
Multifaceted interactions mediated by intrinsically disordered regions play key roles in alpha synuclein aggregation	29
Chromatin compaction by Polycomb group proteins revisited	28
Towards an atomic model of a beating ciliary axoneme	27
Graph neural network approaches for drug-target interactions	27
Finding functional motifs in protein sequences with deep learning and natural language models	27
Metamorphic proteins and how to find them	27
Generative artificial intelligence for de novo protein design	26
Impact of ancestral sequence reconstruction on mechanistic and structural enzymology	26
Advances in machine learning for directed evolution	26
Systematic design of biomolecular force fields	25
Major advances in protein function assignment by remote homolog detection with protein language models – A review	25
Recent advances on the inhibition of human solute carriers: Therapeutic implications and mechanistic insights	25
Advancing protein structure prediction beyond AlphaFold2	25
Protein disaggregation machineries in the human cytosol	25
β-barrel membrane proteins fold via hybrid-barrel intermediate states	25
Deep learning methods for proteome-scale interaction prediction	25
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations	24
Structural insights into the membrane chaperones for multi-pass membrane protein biogenesis	24
Editorial overview: ‘The amazing power of physics to provide chemical insight into catalysis and regulation’ … something better …	24
Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates	24
Editorial overview: Theory and simulation: Molecular modeling from atoms to complexes	24
Editorial overview: Restructuring drug design and development	24
Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them	23
Table of contents	23
Editorial overview: Engineering, evolving, and designing proteins	23
Table of contents	23
Editorial Board	23
Deciphering the dynamic codes: Advances in biomolecular modeling and simulation	23
Editorial overview: Protein–carbohydrate complexes and glycosylation	23
Table of contents	23
Editorial overview: Sequences and topology: ‘paths from sequence to structure’	23
Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries	22
Cryo-EM of the injectisome and type III secretion systems	22
Post-COVID highlights: Challenges and solutions of artificial intelligence techniques for swift identification of COVID-19	22
Generative deep learning for macromolecular structure and dynamics	22
Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing	22
Recent advances in the structural biology of tyrosine kinases	22
The role of water in ligand binding	22
Structural dynamics bridge the gap between the genetic and functional levels of GPCRs	22
Editorial overview: Theory and simulation and their new friends	22
Conformational entropy in molecular recognition of intrinsically disordered proteins	22
Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics	22
Designing better enzymes: Insights from directed evolution	21
A structural framework for DNA replication and transcription through chromatin	21
Diversity of function and mechanism in a family of organic anion transporters	21
Advances in the study of GPCRs by 19F NMR	21
Editorial overview: New insights and complexities for chromatin interacting proteins	21
Insane in the membrane: developments in protein folding, protein transport, and signaling by GPCRs	21
Inner workings of RAG recombinase and its specialization for adaptive immunity	21
Protein N-glycosylation and O-mannosylation are catalyzed by two evolutionarily related GT-C glycosyltransferases	21
Recent developments in multiscale free energy simulations	21
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence	20
Solution NMR investigations of integral membrane proteins: Challenges and innovations	20
Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology	20
RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases	20

Editorial Overview: Protein-nucleic acid Interactions	20
Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography	20
Modelling the assembly and flexibility of antibody structures	20
Structure of the nuclear pore complex goes atomic	20
Modeling membranes in situ	20
Decipher enzymes from human microbiota for drug discovery and development	20
Frontiers in metalloprotein crystallography and cryogenic electron microscopy	20
Mechanical forces and the 3D genome	20
Artificial intelligence for high content imaging in drug discovery	19
Structural and dynamic studies of chromatin by solid-state NMR spectroscopy	19
Exascale simulations and beyond	19
Structure-based discovery and rational design of microtubule-targeting agents	19
Advances in optimizing enzyme electrostatic preorganization	19
Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations	19
Multiscale simulations of protein and membrane systems	19
Empowering the molecular ruler techniques with unnatural base pair system to explore conformational dynamics of flaviviral RNAs	19
Applications of cryo-EM in drug development for STING	19
Graphene in cryo-EM specimen optimization	19
Recent developments in catalysis and inhibition of the Jumonji histone demethylases	19
Challenges, advances, and opportunities in RNA structural biology by Cryo-EM	19
RNA polymerase II elongation factors use conserved regulatory mechanisms	19
Tandem-repeat proteins conformational mechanics are optimized to facilitate functional interactions and complexations	19
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases	19
Conformational penalties: New insights into nucleic acid recognition	19
The method in the madness: Transcriptional control from stochastic action at the single-molecule scale	19
Dynamics, allostery, and stabilities of whole virus particles by amide hydrogen/deuterium exchange mass spectrometry (HDXMS)	19
Structural insights into host–microbe glycointeractions	19
Editorial overview: Engineering and design	18
Editorial Board	18
The “three body solution”: Structural insights into molecular glues	18
Principles of nucleosome recognition by chromatin factors and enzymes	18
Protein folding by the CCT/TRiC chaperone complex	18