Protein p K a Prediction by Tree-Based Machine Learning

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Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines

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A New Solution Structure of ATP Synthase Subunit c from Thermophilic Bacillus PS3, Suggesting a Local Conformational Change for H+-Translocation

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Microscopic mechanisms that govern the titration response and p K a values of buried residues in staphylococcal nuclease mutants

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Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone

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Conformational Reorganization Coupled to the Ionization of Internal Lys Residues in Proteins

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Reservoir pH replica exchange.

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Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water

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A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease

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pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

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Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

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pH-Dependent Transient Conformational States Control Optical Properties in Cyan Fluorescent Protein

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Prediction of pK(a) values of neutral and alkaline drugs with particle swarm optimization algorithm and artificial neural network

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Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

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A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

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Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi

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Determinants of conductance of a bacterial voltage-gated sodium channel

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pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

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A Hierarchical Approach to Predict Conformation-Dependent Histidine Protonation States in Stable and Flexible Proteins

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pH-Dependent Conformational Changes Lead to a Highly Shifted p K a for a Buried Glutamic Acid Mutant of SNase

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Protein pKa prediction with machine learning

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pKAI: a fast and interpretable deep learning approach for accurate electrostatics-driven pKa predictionsPreprint

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Prediction of Protein pKa with Representation LearningPreprint

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AlphaFold, Artificial Intelligence (AI), and Allostery

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Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

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AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function

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Toward an Integrated Machine Learning Model of a Proteomics Experiment

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A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven pKa Predictions in Proteins

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Basis for Accurate Protein p <i>K</i> _a Prediction with Machine Learning

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Benchmarking In Silico Tools for Cysteine p K a Prediction

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Accurately Predicting Protein p K a Values Using Nonequilibrium Alchemy

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Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning

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Accurate and Rapid Prediction of Protein p <i>K</i> _a : Protein Language Models Reveal the Sequence–p <i>K</i> _a Relationship

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Explainable Graph Neural Networks with Data Augmentation for Predicting p K a of C–H Acids

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KaMLs for Predicting Protein p K a Values and Ionization States: Are Trees All You Need?

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Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation

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Structure-based rational design of covalent probes

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Machine learning-augmented metaproteomics reveals metabolic adaptation of anammox bacteria under high nitrogen loading rate

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Swarm Smart Meta-Estimator for 2D/2D Heterostructure Design

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PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins

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Ionizable networks mediate pH-dependent allostery in the SH2 domain–containing signaling proteins SHP2 and SRC

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Machine Learning Isotropic g Values of Radical Polymers

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Feature-Driven Prediction of HOMO–LUMO Gaps in Transition-Metal Complexes Using the SLEET Model: A SMILES-Based Transformer Framework

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pKa prediction for small molecules: an overview of experimental, quantum, and machine learning-based approaches

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Progress in protein pKa prediction

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Machine Learning on the Impacts of Mutations in the SARS-CoV-2 Spike RBD on Binding Affinity to Human ACE2 Based on Deep Mutational Scanning Data

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Recent advances in AI-driven pKa prediction for proteins and small molecules

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Modeling pH-Dependent Protein Dynamics by Integrating Coarse-Grained Molecular Simulation and the Deep Neural Network Model

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Constant-pH Simulation Methods for Biomolecular Systems

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pKAI: a fast and interpretable deep learning approach for accurate electrostatics-driven pKa predictionsPreprint

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Prediction of HPV status in oropharyngeal squamous cell carcinoma based on radiomics and machine learning algorithms: a multi-cohort studyPreprint

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Computationally guided strategies to modulate enzyme pH profiles for industrial biocatalysis and environmental applications

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MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins

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Exploring non-invasive biomarkers for pulmonary nodule detection based on salivary microbiomics and machine learning algorithms

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A fast and interpretable deep learning approach for accurate electrostatics-driven pKa predictions in proteinsPreprint

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Ionizable networks mediate pH-dependent allostery in SH2 signaling proteinsPreprint

Dyck, P. K. V., Piszkin, L. J., Gorski, E. A., Nascimento, E. T., Abebe, J. A., Hoffmann, L. M., Peng, J. W., & White, K. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.21.608875

ME-p K a : A Deep Learning Method with Multimodal Learning for Protein p K a Prediction

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ZHMolTopoRPI: A Commutative Algebra-Driven Deep Learning Framework for Robust RNA-Protein Interaction Prediction

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Machine Learning in Predicting the Physicochemical Properties of Drug Candidates

Nuthi, A., & Dixit, V. A. (2026) · Royal Society of Chemistry eBooks · doi:10.1039/9781837070206-00280

DeepKa Protein pKa Database: Identifying pH Dependence in the Protein Data Bank.

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KaMLs for Predicting Protein p K a Values and Ionization States: Are Trees All You Need?

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Basis for Accurate Protein p <i>K</i> _a Prediction with Machine Learning

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ME-p K a : A Deep Learning Method with Multimodal Learning for Protein p K a Prediction

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Accurate and Rapid Prediction of Protein p <i>K</i> _a : Protein Language Models Reveal the Sequence–p <i>K</i> _a Relationship

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