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Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning

Journal of chemical information and modeling, 2024-05, Vol.64 (10), p.4310-4321

2024

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Ensemble Models Based on QuBiLS-MAS Features and Shallow Learning for the Prediction of Drug-Induced Liver Toxicity: Improving Deep Learning and Traditional Approaches

Chemical research in toxicology, 2020-07, Vol.33 (7), p.1855-1873

2020

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Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set

Journal of chemical information and modeling, 2021-06, Vol.61 (6), p.3141-3157

2021

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Examining evolutionary scale modeling‐derived different‐dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow

Protein science, 2024-04, Vol.33 (4), p.e4928-n/a

2024

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MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors

Journal of chemical information and modeling, 2020-02, Vol.60 (2), p.1042-1059

2020

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Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints

Molecular informatics, 2023-06, Vol.42 (6), p.e2200227-n/a

2023

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Distributed and multicore QuBiLS‐MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Journal of computational chemistry, 2020-05, Vol.41 (12), p.1209-1227

2020

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Enhancing Acute Oral Toxicity Predictions by using Consensus Modeling and Algebraic Form-Based 0D-to-2D Molecular Encodes

Chemical research in toxicology, 2019-06, Vol.32 (6), p.1178-1192

2019

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QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Journal of cheminformatics, 2017-06, Vol.9 (1), p.35-35, Article 35

2017

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Constraining the Prebiotic Cell Size Limits in Extremely Hostile Environments: A Dynamical Perspective

Astrobiology, 2018-04, Vol.18 (4), p.403-411

2018

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Fuzzy spherical truncation-based multi-linear protein descriptors: From their definition to application in structural-related predictions

Frontiers in chemistry, 2022-10, Vol.10, p.959143-959143

2022

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Do deep learning models make a difference in the identification of antimicrobial peptides?

Briefings in bioinformatics, 2022-05, Vol.23 (3)

2022

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Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach

Scientific reports, 2020-10, Vol.10 (1), p.18074-18074, Article 18074

2020

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Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)

Journal of cheminformatics, 2018-10, Vol.10 (1), p.51-17, Article 51

2018

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Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?

Briefings in bioinformatics, 2022-11, Vol.23 (6)

2022

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Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3736-3736

2021

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LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: Theory and validation by QSARs

Journal of theoretical biology, 2020-01, Vol.485, p.110039-110039, Article 110039

2020

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Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes

Journal of theoretical biology, 2015-06, Vol.374, p.125-137

2015

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IMMAN: free software for information theory-based chemometric analysis

Molecular diversity, 2015-05, Vol.19 (2), p.305-319

2015

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Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions

Physical chemistry chemical physics : PCCP, 2020-05, Vol.22 (17), p.9283-9289

2020

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Database fingerprint (DFP): an approach to represent molecular databases

Journal of cheminformatics, 2017-02, Vol.9 (1), p.9-9, Article 9

2017

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StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks

Bioinformatics (Oxford, England), 2023-08, Vol.39 (8)

2023

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Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks

NPJ systems biology and applications, 2024-10, Vol.10 (1), p.115-18, Article 115

2024

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Pharmacophoric sites of anticancer metal complexes located using quantum topological atomic descriptors

Journal of molecular structure, 2020-03, Vol.1204, p.127480, Article 127480

2020

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Drug repositioning for novel antitrichomonas from known antiprotozoan drugs using hierarchical screening

Future medicinal chemistry, 2018-04, Vol.10 (8), p.863-878

2018

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Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning

Ensemble Models Based on QuBiLS-MAS Features and Shallow Learning for the Prediction of Drug-Induced Liver Toxicity: Improving Deep Learning and Traditional Approaches

Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set

Examining evolutionary scale modeling‐derived different‐dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow

MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors

Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints

Distributed and multicore QuBiLS‐MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Enhancing Acute Oral Toxicity Predictions by using Consensus Modeling and Algebraic Form-Based 0D-to-2D Molecular Encodes

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Constraining the Prebiotic Cell Size Limits in Extremely Hostile Environments: A Dynamical Perspective

Fuzzy spherical truncation-based multi-linear protein descriptors: From their definition to application in structural-related predictions

Do deep learning models make a difference in the identification of antimicrobial peptides?

Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach

Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)

Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?

Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set

LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: Theory and validation by QSARs

Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes

IMMAN: free software for information theory-based chemometric analysis

Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions

Database fingerprint (DFP): an approach to represent molecular databases

StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks

Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks

Pharmacophoric sites of anticancer metal complexes located using quantum topological atomic descriptors

Drug repositioning for novel antitrichomonas from known antiprotozoan drugs using hierarchical screening

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