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Very fast prediction and rationalization of pKa values for protein-ligand complexes

Proteins, structure, function, and bioinformatics, 2008-11, Vol.73 (3), p.765-783

2008

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Prediction of pKa Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2017-01, Vol.121 (3), p.699-707

2017

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Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

BMC structural biology, 2011-01, Vol.11 (1), p.6-6, Article 6

2011

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Prediction of pKa values using the PM6 semiempirical method

PeerJ (San Francisco, CA), 2016-08, Vol.4, p.e2335-e2335, Article e2335

2016

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In silico prediction of mutant HIV-1 proteases cleaving a target sequence

PloS one, 2014-05, Vol.9 (5), p.e95833-e95833

2014

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Effects of buffer composition and dilution on nanowire field-effect biosensors

Nanotechnology, 2013-01, Vol.24 (3), p.035501-1-9

2013

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A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H

PeerJ (San Francisco, CA), 2014-06, Vol.2, p.e449-e449

2014

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Towards a barrier height benchmark set for biologically relevant systems

PeerJ (San Francisco, CA), 2016-05, Vol.4, p.e1994-e1994, Article e1994

2016

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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

Nucleic acids research, 2007-07, Vol.35 (Web Server issue), p.W522

2007

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ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

PeerJ (San Francisco, CA), 2015-10, Vol.3, p.e1344-e1344, Article e1344

2015

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FTIR Spectroscopy Combined with Isotope Labeling and Quantum Chemical Calculations to Investigate Adsorbed Bicarbonate Formation Following Reaction of Carbon Dioxide with Surface Hydroxyl Groups on Fe2O3 and Al2O3

The journal of physical chemistry. B, 2006-06, Vol.110 (24), p.12005-12016

2006

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Prediction and Rationalization of the pH Dependence of the Activity and Stability of Family 11 Xylanases

Biochemistry (Easton), 2007-11, Vol.46 (47), p.13581-13592

2007

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Bayesian inference of protein structure from chemical shift data

PeerJ (San Francisco, CA), 2015-03, Vol.3, p.e861-e861

2015

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Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase

Computational and structural biotechnology journal, 2015-01, Vol.13 (C), p.256-264

2015

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FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

PeerJ (San Francisco, CA), 2014-03, Vol.2, p.e277-e277

2014

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Using a genetic algorithm to find molecules with good docking scores

PeerJ physical chemistry, 2021-05, Vol.3, p.e18, Article e18

2021

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Fast and automated identification of reactions with low barriers using meta-MD simulations

PeerJ physical chemistry, 2022-03, Vol.4, p.e22, Article e22

2022

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pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides

Journal of chemical information and modeling, 2017-08, Vol.57 (8), p.1723-1727

2017

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Genetic algorithm-based re-optimization of the Schrock catalyst for dinitrogen fixation

PeerJ physical chemistry, 2023-12, Vol.5, p.e30, Article e30

2023

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Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations

PeerJ physical chemistry, 2020-09, Vol.2, p.e15, Article e15

2020

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Calculating pH and salt dependence of protein-protein binding

Current pharmaceutical biotechnology, 2008-04, Vol.9 (2), p.96

Jensen, Jan H

2008

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Chemical space exploration: how genetic algorithms find the needle in the haystack

PeerJ physical chemistry, 2020-07, Vol.2, p.e11, Article e11

2020

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Protein-protein binding is often associated with changes in protonation state

Proteins, structure, function, and bioinformatics, 2008-04, Vol.71 (1), p.81-91

2008

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The determinants of carboxyl pKa values in turkey ovomucoid third domain

Proteins, structure, function, and bioinformatics, 2004-05, Vol.55 (3), p.689-704

2004

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High throughput virtual screening of 230 billion molecular solar heat battery candidates

PeerJ physical chemistry, 2021-02, Vol.3, p.e16, Article e16

2021

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

Prediction of pKa Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods

Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

Prediction of pKa values using the PM6 semiempirical method

In silico prediction of mutant HIV-1 proteases cleaving a target sequence

Effects of buffer composition and dilution on nanowire field-effect biosensors

A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H

Towards a barrier height benchmark set for biologically relevant systems

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

FTIR Spectroscopy Combined with Isotope Labeling and Quantum Chemical Calculations to Investigate Adsorbed Bicarbonate Formation Following Reaction of Carbon Dioxide with Surface Hydroxyl Groups on Fe2O3 and Al2O3

Prediction and Rationalization of the pH Dependence of the Activity and Stability of Family 11 Xylanases

Bayesian inference of protein structure from chemical shift data

Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

Using a genetic algorithm to find molecules with good docking scores

Fast and automated identification of reactions with low barriers using meta-MD simulations

pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides

Genetic algorithm-based re-optimization of the Schrock catalyst for dinitrogen fixation

Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations

Calculating pH and salt dependence of protein-protein binding

Chemical space exploration: how genetic algorithms find the needle in the haystack

Protein-protein binding is often associated with changes in protonation state

The determinants of carboxyl pKa values in turkey ovomucoid third domain

High throughput virtual screening of 230 billion molecular solar heat battery candidates

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