Computational Theory and Mathematics papers
Pofolia’s corpus holds 91 papers from Computational Theory and Mathematics (2012–2026), each with a short summary. Below, the 20 most-cited, then the most recently added.
At a glance
- Most cited: SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules (2017, 17,339 citations).
- The 20 papers listed have 110,694 citations between them.
- 13 of the 13 with a known journal quartile appeared in a Q1 journal.
- 12 have a free full text (open access).
- Most frequent journals: Nucleic Acids Research, Cambridge University Press eBooks, Journal of Chemical Information and Modeling.
- Published between 2012 and 2021.
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”. How to read the signals
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 · Open access
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.
Disordered electronic systems
Cambridge University Press eBooks · 2012 · FWCI 168.48 · 3,271 citations
This book chapter provides a comprehensive overview of disordered electronic systems, a fundamental topic in condensed matter physics and materials science.
Recently added
Regularisation of regression trees by summation of p values
Computational Statistics · 2026 · Q2
A new deterministic, in-sample method for stopping the growth of CART regression trees uses node-wise p-value summation, offering an alternative to time-consuming cross-validation.
Scalable molecular representations enabled by multimodal fusion and sequence distillation
Nature Communications · 2026 · Q1 · SJR 4.00
A new 'Chemical Dice Integrator' unifies six molecular views into a single latent space, distilled into a sequence-based model for direct embedding from molecular strings, outperforming classical fusion and established descriptors in prediction benchmarks.
A leakage-aware and auditable framework prioritizes class I HDAC inhibitors for pan-cancer transcriptomic reversal
BMC Bioinformatics · 2026 · Q1 · SJR 1.00
A conventional fingerprint MLP comparator outperformed a dual-stream atom-token/fingerprint model in predicting transcriptomic reversal for pan-cancer HDAC inhibitors, with signed wTRS enriching class I HDACs (fold enrichments 4.62-30.6, FDR < 10^-4).
A PTAS for triangle-free 2-matching
Mathematical Programming · 2026 · Q1 · SJR 2.00
A new, simpler Polynomial Time Approximation Scheme (PTAS) is presented for the Triangle-Free 2-Matching problem, achieving near-optimal solutions.
Lower Bounds for Set-Multilinear Branching Programs
SIAM Journal on Computing · 2026 · Q1 · Open access
Researchers proved super-polynomial lower bounds for sums of ordered set-multilinear algebraic branching programs (ABPs) for low-degree polynomials, marking the first such bound in this regime and generalizing Nisan's work.
Multiset metric dimension of binomial random graphs
Discrete Applied Mathematics · 2026 · Q2
We establish bounds for the multiset metric dimension of binomial random graphs G(n, p) with edge probability p such that (n-1)p = \Theta(n^x) for a fixed x in (0,1).
The Virtual Biotech: A multi-agent AI framework for therapeutic discovery and development
Science · 2026 · Q1 · SJR 10.00 · FWCI 5.02 · 1 citations
A multi-agent AI framework, the 'Virtual Biotech,' successfully identified drugs targeting cell-type-specific genes as 48% more likely to reach market with 32% fewer adverse events, based on analysis of 55,984 trials.
Max Weight Independent Set in sparse graphs with no long claws
ACM Transactions on Algorithms · 2026 · Q1 · 1 citations · Open access
A polynomial-time algorithm is presented for the Max Weight Independent Set (MWIS) problem in graphs that exclude specific structures: a fixed forest of paths and subdivided claws as an induced subgraph, and a fixed biclique as a subgraph.
Journals in this field
The journals that publish most of this field’s papers. Quartile (Q1–Q4), SJR and h-index are from SCImago Journal Rank; “in this field” is how many of the journal’s pooled papers belong here. What is a Q1 journal? · What is the h-index?
| Journal | Quartile | SJR | h-index | In this field | Summaries |
|---|---|---|---|---|---|
| Nucleic Acids Research | Q1 | 8.00 | 714 | 20 | 43 |
| Journal of Chemical Information and Modeling | Q1 | 1.00 | 219 | 8 | 14 |
| Journal of Medicinal Chemistry | Q1 | 1.00 | 329 | 4 | 11 |
| Journal of Cheminformatics | Q1 | 1.00 | 101 | 4 | 6 |
| Science | Q1 | 10.00 | 1433 | 3 | 268 |
| IEEE Transactions on Evolutionary Computation | Q1 | 3.00 | 229 | 3 | 3 |
| International Journal of Molecular Sciences | Q1 | 1.00 | 365 | 2 | 45 |
| Annals of Mathematics | Q1 | 9.00 | 153 | 1 | 25 |
Every journal in Computational Theory and Mathematics (Q1–Q4) →
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