Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 3 complete abstracts (539 words), 9 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Structure, Molecular; Molecular Structures; Structures, Molecular.
Where it fits in the MeSH classification
- Broader topics
- Biochemical Phenomena; Chemical Phenomena
- Narrower topics
- Amino Acid Sequence; Base Sequence; Binding Sites; Carbohydrate Sequence; Conserved Sequence; Isomerism; Molecular Conformation; Molecular Dynamics Simulation
- See also
- Models, Molecular
Research landscape
PubMed indexes 1,920,943 records tagged with the MeSH heading “Molecular Structure” (counts retrieved 2026-10-29). 211,075 of them (11.0%) were published from 2020 onward, and the busiest period so far is through 1999 with 599,097 records.
Reviews account for 127,359 records (6.6%) and meta-analyses for 1,376. Randomized controlled trials number 1,347 (0.1%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 599,097 |
| 2000-2009 | 558,720 |
| 2010-2019 | 552,051 |
| 2020 onward | 211,075 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 127,359 | 6.6% |
| Meta-analyses | 1,376 | 0.1% |
| Randomized controlled trials | 1,347 | 0.1% |
Method: PubMed query "Molecular Structure"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in molecular biology
Molecular biology establishes mechanisms through controlled experiments, often in simplified systems such as purified proteins, cultured cells or model organisms. Such work can show what is possible in a defined system, but whether a pathway matters in a whole organism or in human disease needs further evidence. Check the experimental system, whether findings were reproduced by independent groups, and whether the authors tested the mechanism directly or inferred it from correlation.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization | 2026 | Research article Design not recorded in structured metadata | 4 | cc by PMID 42669708 · DOI · PMC13526836 |
| Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease | 2026 | Research article Design not recorded in structured metadata | 2 | cc by PMID 42685224 · DOI · PMC13537272 |
| Investigating enzyme function by geometric matching of catalytic motifs | 2026 | Research article Design not recorded in structured metadata | 2 | cc by PMID 42563495 · DOI · PMC13448135 |
A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization [1]
Abstract reading summary — source excerpts
- Opening excerpt
- Understanding the complex interplay between gene expression and neuronal activity is crucial for unraveling the molecular mechanisms underlying cognitive function and neurological disorders.
- Closing excerpt
- This CRISPRi-based screening platform offers a versatile tool to uncover molecular mechanisms controlling neuronal function in health and disease.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (124 words)
Understanding the complex interplay between gene expression and neuronal activity is crucial for unraveling the molecular mechanisms underlying cognitive function and neurological disorders. Here, we developed pooled screens using CRISPR interference (CRISPRi) and the fluorescent calcium integrator CaMPARI2 to evaluate genetic modifiers of neuronal depolarization. Using this screening method, we evaluated 1343 genes for their effect on depolarization in a human iPSC-derived neuron model, revealing potential links to neurodegenerative and neurodevelopmental disorders. These genes include known regulators of neuronal excitability, such as TARPs and ion channels, as well as genes associated with autism spectrum disorder and Alzheimer's disease not previously described to affect neuronal depolarization. This CRISPRi-based screening platform offers a versatile tool to uncover molecular mechanisms controlling neuronal function in health and disease.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42669708 · DOI · PMC13526836
Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease [2]
Abstract reading summary — source excerpts
- Opening excerpt
- Parkinson's disease (PD) is a neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear.
- Closing excerpt
- Our findings provide insights into TE transcription in the PD brain and suggest that TEs may contribute to neuroinflammation and pathological progression in PD.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (163 words)
Parkinson's disease (PD) is a neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TEs) have been linked to inflammation, but their potential role in PD remains unexplored. Using bulk- and single-nuclei RNA-seq of postmortem brain tissue from four brain regions, we studied TE transcription and its correlation with PD neuroinflammation. Over a thousand TEs, including LINE-1 s and ERVs, were expressed in a cell type- and region-specific manner in the human brain. Increased TE expression was found in microglia and neurons in the substantia nigra and putamen of PD brains, but not amygdala or prefrontal cortex, compared to controls. This TE activation correlated with an innate immune response in the same brain regions. The link between an interferon response and TE activation was mechanistically confirmed using human pluripotent stem cell-derived microglia and neurons. Our findings provide insights into TE transcription in the PD brain and suggest that TEs may contribute to neuroinflammation and pathological progression in PD.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42685224 · DOI · PMC13537272
Investigating enzyme function by geometric matching of catalytic motifs [3]
Abstract reading summary — source excerpts
- Opening excerpt
- The rapidly growing universe of predicted protein structures offers opportunities for data driven exploration but requires computationally scalable and interpretable tools.
- Closing excerpt
- uk/thornton-srv/m-csa/enzymm.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (252 words)
The rapidly growing universe of predicted protein structures offers opportunities for data driven exploration but requires computationally scalable and interpretable tools. We developed a method to detect catalytic features in protein structures, providing insights into enzyme function and mechanism. A library of 6780 3D coordinate sets describing enzyme catalytic sites, referred to as templates, has been collected from manually curated examples of 762 enzyme catalytic mechanisms described in the Mechanism and Catalytic Site Atlas. For template searching we optimized the geometric-matching algorithm Jess. We implemented RMSD and residue orientation filters to differentiate catalytically informative matches from spurious ones. We validated this approach on a non-redundant set of high quality experimental (n = 3751, <40% amino acid identity) enzyme structures with well annotated catalytic sites as well as predicted structures of the human proteome. We show matching catalytic templates solely on structure is more sensitive than sequence- and 3D-structure-based approaches in identifying homology between distantly related enzymes. Since geometric matching does not depend on conserved sequence motifs or even common evolutionary history, we are able to identify examples of structural active site similarity in highly divergent and possibly convergent enzymes. Such examples make interesting case studies into the evolution of enzyme function. Though not intended for characterizing substrate-specific binding pockets, the speed and knowledge-driven interpretability of our method make it well suited for expanding enzyme active-site annotation across large predicted proteomes. We provide the method and template library as a Python module, Enzyme Motif Miner, at https://github.com/rayhackett/enzymm and as a webserver at https://www.ebi.ac.uk/thornton-srv/m-csa/enzymm.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42563495 · DOI · PMC13448135
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article H3K4me3 breadth is linked to cell identity and transcriptional consistency [4]
- Research article Repeated replication and a prospective meta-analysis of the association between chromosome 9p21.3 and coronary artery disease [5]
- Research article Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism [6]
- Research article DNA methylation in childhood asthma: an epigenome-wide meta-analysis [7]
- Research article Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease [8]
- Research article Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis [9]
References
- Boggess SC, Gandhi V, Tsai MC, Marzette E, Teyssier N, Chou JY, et al.. A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization. . 2026. PMID 42669708 · DOI · PMC13526836
- Garza R, Adami A, Thiruvalluvan A, Wijesinghe S, Curle A, Tam O, et al.. Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease. . 2026. PMID 42685224 · DOI · PMC13537272
- Hackett RE, Riziotis IG, Larralde M, Ribeiro AJM, Zeller G, Thornton JM. Investigating enzyme function by geometric matching of catalytic motifs. . 2026. PMID 42563495 · DOI · PMC13448135
- Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, et al.. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 2014. PMID 25083876 · DOI · PMC4137894
- Schunkert H, Götz A, Braund P, McGinnis R, Tregouet DA, Mangino M, et al.. Repeated replication and a prospective meta-analysis of the association between chromosome 9p21.3 and coronary artery disease. Circulation. 2008. PMID 18362232 · DOI · PMC2689930
- Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, et al.. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature. 2015. PMID 26560027 · DOI · PMC4775078
- Xu CJ, Söderhäll C, Bustamante M, Baïz N, Gruzieva O, Gehring U, et al.. DNA methylation in childhood asthma: an epigenome-wide meta-analysis. Lancet Respir Med. 2018. PMID 29496485 · DOI
- Agha G, Mendelson MM, Ward-Caviness CK, Joehanes R, Huan T, Gondalia R, et al.. Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. Circulation. 2019. PMID 31424985 · DOI · PMC6812683
- Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, et al.. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med. 2015. PMID 25849352 · DOI · PMC4388826
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.