Lessons from 60 Years of the Journal of Chemical Information and Modeling
What gives a scientific paper lasting influence? Why do some research articles become foundational touchstones cited by thousands of subsequent studies, while others fade into obscurity?
The Journal of Chemical Information and Modeling (JCIM) provides a perfect case study to explore these questions, with its 60-year history offering a window into the evolution of scientific impact in chemical informatics and molecular modeling .
Current Impact Factor
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Years of Publication
Through examining patterns across JCIM's history and analyzing its most cited works, we can uncover the recipe for scientific impact that extends far beyond a single discipline.
Scientific influence can be measured in multiple dimensions, and JCIM's metrics reveal a story of growing relevance in an increasingly computational world.
The journal's SCImago Journal Rank (SJR) has fluctuated between 1.223 and 1.575 over the past decade, settling at 1.467 in 2024, reflecting its consistent standing as a Q1 journal in multiple categories including chemical engineering, chemistry, computer science applications, and library and information sciences 1 2 .
Perhaps more telling is the dramatic increase in publications the journal has handled. From publishing approximately 150-300 papers annually in its earlier years, JCIM now publishes nearly 800 papers per year 2 . This growth mirrors the expansion of computational approaches across chemical research.
Analysis of JCIM's most influential papers reveals several common characteristics that transcend their specific technical contributions.
The most cited paper in JCIM's history is the ZINC database article with 2,765 citations, which described a free database of commercially available compounds for virtual screening 6 . This paper addressed a critical bottleneck for drug discovery researchers.
JCIM's scope sits at the intersection of multiple fields, and its most influential papers often build bridges between traditionally separate disciplines. The journal's top research topics include artificial intelligence, computational biology, and molecular dynamics 6 .
Highly cited papers frequently lower barriers to entry for computational methods. The ZINC database paper provided free access to screening compounds, democratizing research capabilities that were previously limited to well-funded laboratories 7 .
Papers that introduce novel methodologies rather than reporting incremental improvements tend to accumulate citations more rapidly. The development of extended-connectivity fingerprints provided a fundamentally new way to represent molecular structures 6 .
| Paper Title | Citation Count | Year | Primary Contribution |
|---|---|---|---|
| ZINC - A Free Database of Commercially Available Compounds for Virtual Screening | 2,765 | 2005 | Created accessible compound database |
| LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery | 2,491 | 2011 | Developed accessible visualization tool |
| Extended-Connectivity Fingerprints | 2,420 | 2010 | Introduced novel molecular representation |
Data sourced from 6
The creation of the ZINC database represented a mammoth curation effort involving the assembly, organization, and standardization of commercially available chemical compounds. The researchers focused on compiling compounds that were immediately accessible for virtual screening.
From multiple commercial suppliers
Of structural representations using consistent formats
Of molecular properties relevant to drug discovery
Of user-friendly search and browsing interfaces
Of regular update cycles to maintain database relevance
Compounds
The initial ZINC database contained approximately 4.6 million compounds, each represented in multiple formats suitable for different computational approaches 6 . This comprehensive collection immediately became indispensable for virtual screening—a technique where compound libraries are computationally tested against biological targets to identify potential drug candidates.
The ZINC database paper exemplifies several principles of high-impact research:
The resource was designed to grow, ensuring long-term relevance
By being freely available, it lowered barriers to entry
Support for multiple file formats made it useful across platforms
It solved an immediate, widespread problem in drug discovery
Based on analysis of highly cited papers in JCIM, several methodological approaches and resources consistently appear in influential research.
Predicting how molecules bind to targets
Virtual ScreeningRelating chemical structure to biological activity
Predictive ModelsSimulating physical movements of atoms and molecules
Protein InteractionsExtracting patterns from chemical data
Property PredictionStoring and retrieving chemical information
ZINC, PubChemRepresenting molecular structures and interactions
LigPlot+Recent highly cited papers in JCIM increasingly feature artificial intelligence and machine learning approaches 6 . The integration of these technologies represents a significant shift in methodology.
The movement toward "increasing openness of chemical data, driven by initiatives promoting public databases such as PubChem and ChEMBL" 7 has created an environment where papers that provide accessible data accumulate citations rapidly.
As we look ahead, the factors driving high citation counts continue to evolve. The integration of artificial intelligence represents perhaps the most significant shift, with machine learning approaches rapidly becoming standard methodology rather than novel innovations 7 .
Papers that effectively bridge traditional chemical expertise with cutting-edge computational approaches are likely to dominate the citation landscape.
Recent special collections have focused on "Improving Reproducibility and Reusability" 3 , suggesting that papers emphasizing these values may gain increased recognition.
As chemoinformatics methodologies find applications in "drug discovery, materials science, and environmental chemistry" 7 , papers that transfer approaches between domains attract broad citation networks.
The recipe for a highly cited paper in chemical informatics combines technical innovation with practical utility. Across 60 years of JCIM publications, the most influential papers share common traits: they solve widespread research problems, bridge disciplinary divides, enhance accessibility, and provide foundational methodologies upon which others can build.