Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states

Reservoir pH replica exchange

(2018) Ana Damjanovic et al.   JOURNAL OF CHEMICAL PHYSICS

The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory

(2018) Nicolas Tielker et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge

(2018) Qiao Zeng et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge

(2018) Philipp Pracht et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies

(2018) Edithe Selwa et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL6 challenge results from pKa predictions based on a general Gaussian process model

(2018) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

(2018) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge

(2018) Samarjeet Prasad et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

(2016) Frank C. Pickard et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology To Improve in Silico pKa Prediction

(2014) Robert Fraczkiewicz et al.   Journal of Chemical Information and Modeling

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Recent development and application of constant pH molecular dynamics

(2014) Wei Chen et al.   MOLECULAR SIMULATION

Who cares for the protons?

(2012) Paul Czodrowski   BIOORGANIC & MEDICINAL CHEMISTRY

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

(2010) Jeremy R. Greenwood et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predicting pKa

(2009) Adam C. Lee et al.   Journal of Chemical Information and Modeling

Let’s not forget tautomers

(2009) Yvonne Connolly Martin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN