Key papers in Computational Theory and Mathematics
Pofolia’s corpus holds 74 papers from the Computational Theory and Mathematics subfield (2012–2026). The list below starts with the most cited.
Most cited
Ranked by citation count. Because citations accumulate over time, this list naturally leans towards work published a few years ago; for where the field is now, see “recently added”.
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
Scientific Reports · 2017 · Q1 · FWCI 340.43 · 17,339 citations · Open access
A new free web tool, SwissADME, has been developed to rapidly predict key drug properties like pharmacokinetics and drug-likeness for small molecules using computational models.
DrugBank 5.0: a major update to the DrugBank database for 2018
Nucleic Acids Research · 2017 · Q1 · SJR 8.00 · FWCI 409.07 · 8,859 citations · Open access
DrugBank 5.0, a significant upgrade to the comprehensive drug information database, has expanded its content by up to 100% or more in many areas, including a nearly 600% increase in drug-drug interactions.
Random search for hyper-parameter optimization
2012 · FWCI 113.55 · 7,939 citations
Random search is empirically and theoretically more efficient for hyper-parameter optimization than grid search, finding equally good or better models in less computation time.
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
Journal of Chemical Information and Modeling · 2021 · Q1 · SJR 1.00 · FWCI 405.50 · 6,839 citations
AutoDock Vina 1.2.0 now supports macrocycle and explicit water molecule modeling, previously a limitation compared to other AutoDock programs.
An Evolutionary Many-Objective Optimization Algorithm Using Reference-Point-Based Nondominated Sorting Approach, Part I: Solving Problems With Box Constraints
IEEE Transactions on Evolutionary Computation · 2013 · Q1 · SJR 3.00 · FWCI 126.54 · 6,837 citations
A new evolutionary algorithm, NSGA-III, is proposed for many-objective optimization problems (4+ objectives), outperforming existing methods on test problems with up to 15 objectives.
PubChem Substance and Compound databases
Nucleic Acids Research · 2015 · Q1 · SJR 8.00 · FWCI 318.36 · 5,504 citations · Open access
PubChem, a public repository for chemical substance and biological activity data, has grown significantly since its 2004 launch, now serving as a key resource for researchers.
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures
Journal of Medicinal Chemistry · 2015 · Q1 · SJR 1.00 · FWCI 40.46 · 5,474 citations · Open access
A new computational tool, pkCSM, utilizes graph-based signatures to predict key drug pharmacokinetic and toxicity properties, performing comparably to or better than existing methods.
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Expert Opinion on Drug Discovery · 2015 · Q1 · SJR 1.00 · FWCI 155.50 · 5,329 citations · Open access
MM/PBSA and MM/GBSA methods are popular for estimating ligand-binding affinities, offering a balance between accuracy and computational cost compared to simpler or more complex methods.
TCMSP: a database of systems pharmacology for drug discovery from herbal medicines
Journal of Cheminformatics · 2014 · Q1 · SJR 1.00 · FWCI 37.39 · 5,064 citations · Open access
The TCMSP database integrates pharmacochemistry, ADME properties, targets, and diseases for 499 Chinese herbs, enabling systems pharmacology analysis for drug discovery.
Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation
arXiv (Cornell University) · 2020 · 4,431 citations · Open access
Commonly used evaluation measures like Precision, Recall, and F-Measure are biased and can misrepresent system performance, potentially showing worse systems as better.
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules
Nucleic Acids Research · 2019 · Q1 · SJR 8.00 · FWCI 191.43 · 4,306 citations · Open access
The updated SwissTargetPrediction web tool now predicts small molecule protein targets using a larger database of 376,342 compounds and 3,068 targets, achieving over 70% accuracy in identifying at least one correct human target within the top 15 predictions.
Matrix Analysis
Cambridge University Press eBooks · 2012 · FWCI 13.89 · 4,303 citations
This second edition of an acclaimed text offers a revised and updated exploration of linear algebra and matrix theory, unifying classic and recent results through canonical forms.
PubChem in 2021: new data content and improved web interfaces
Nucleic Acids Research · 2020 · Q1 · SJR 8.00 · FWCI 320.72 · 4,014 citations · Open access
PubChem, a major chemical information resource, has significantly expanded its data by integrating over 100 new sources and launched new features like a Periodic Table and Pathway pages.
Personal Communication
2014 · FWCI 599.33 · 3,824 citations
A novel two-dimensional method is presented to determine lightness from image intensity by exploiting differences in the spatial distribution of reflectance and illumination components.
Mathematical Theory of Optimal Processes
2018 · FWCI 55.11 · 3,721 citations
This volume introduces the maximum principle as a universal solution for a broad class of variational problems, extending beyond classical calculus of variations.
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
Science · 2020 · Q1 · SJR 10.00 · FWCI 397.80 · 3,442 citations · Open access
The crystal structure of the SARS-CoV-2 main protease (Mpro) has been determined, revealing its complex with an improved α-ketoamide inhibitor. This structural insight enables the design of potent Mpro inhibitors with enhanced plasma half-life and lung tropism.
PubChem 2019 update: improved access to chemical data
Nucleic Acids Research · 2018 · Q1 · SJR 8.00 · FWCI 314.26 · 3,406 citations · Open access
PubChem has released significant updates, enhancing access to chemical data with new content and improved web and programmatic interfaces.
ZINC 15 – Ligand Discovery for Everyone
Journal of Chemical Information and Modeling · 2015 · Q1 · SJR 1.00 · FWCI 76.26 · 3,401 citations
ZINC 15 is a new version of a ligand database that now includes over 120 million purchasable compounds, aiming to make chemical information accessible to biologists without specialized informatics training.
Conjectures and Refutations
MQUP eBooks · 2020 · FWCI 57.75 · 3,391 citations
Conjectures are not merely failures to prove theorems but an essential and rational part of mathematical research, driving progress through trial and error.
Fundamentals of Domination in Graphs
2013 · 3,302 citations
This work offers the first comprehensive overview of domination in graphs, covering theoretical, algorithmic, and application aspects.
Recently added
Givenness, Contrastiveness, Definiteness, Subjects, Topics, and Point of View
2026 · FWCI 314.63 · 1,846 citations
This paper explores the multifaceted roles a noun can play within a sentence, extending beyond traditional grammatical functions.
DrugBank 6.0: the DrugBank Knowledgebase for 2024
Nucleic Acids Research · 2023 · Q1 · SJR 8.00 · FWCI 228.97 · 1,579 citations · Open access
DrugBank 6.0, released in 2024, significantly expands its drug knowledgebase, increasing FDA-approved drugs by 72% (to 4563), investigational drugs by 38% (to 6231), drug-drug interactions by 300% (to 1,413,413), and drug-food interactions by 200% (to 2475).
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
Nucleic Acids Research · 2023 · Q1 · SJR 8.00 · FWCI 332.25 · 2,273 citations · Open access
antiSMASH 7.0 significantly improves microbial genome mining by increasing supported biosynthetic gene cluster (BGC) types from 71 to 81, enhancing chemical structure prediction, and refining visualization of enzymatic assembly lines and gene cluster regulation.
A Dynamic Survey of Graph Labeling
The Electronic Journal of Combinatorics · 2022 · Q1 · FWCI 47.58 · 2,190 citations
This survey consolidates over 200 graph labeling techniques, drawing from more than 3000 papers published since the mid-1960s, to address the difficulty of tracking research in this field.
PubChem 2023 update
Nucleic Acids Research · 2022 · Q1 · SJR 8.00 · FWCI 367.86 · 3,238 citations · Open access
PubChem has integrated Google Patents data, created new Cell Line and Taxonomy collections, updated its bioassay data model, and enhanced programmatic access with target-centric downloads and structure standardization.
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