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A graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space

Chemical science (Cambridge), 2019-03, Vol.10 (12), p.3567-3572

Jensen, Jan H

2019

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Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values

Journal of chemical theory and computation, 2011-07, Vol.7 (7), p.2284-2295

2011

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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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Improving solvation energy predictions using the SMD solvation method and semiempirical electronic structure methods

The Journal of chemical physics, 2018-09, Vol.149 (10), p.104102-104102

2018

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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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Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions

Chemical science (Cambridge), 2018, Vol.9 (3), p.660-665

2018

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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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Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry

PloS one, 2013-04, Vol.8 (4), p.e60602-e60602

2013

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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2010-08, Vol.114 (33), p.8705-8712

2010

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FragIt: a tool to prepare input files for fragment based quantum chemical calculations

PloS one, 2012-09, Vol.7 (9), p.e44480-e44480

2012

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The effective fragment molecular orbital method for fragments connected by covalent bonds

PloS one, 2012-07, Vol.7 (7), p.e41117-e41117

2012

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Fully Integrated Effective Fragment Molecular Orbital Method

Journal of chemical theory and computation, 2013-05, Vol.9 (5), p.2235-2249

2013

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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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The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2001-01, Vol.105 (2), p.293-307

2001

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Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

Journal of computational chemistry, 2010-03, Vol.31 (4), p.778-790

2010

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Determinants of the Relative Reduction Potentials of Type-1 Copper Sites in Proteins

Journal of the American Chemical Society, 2004-06, Vol.126 (25), p.8010-8019

2004

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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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PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

Journal of computational chemistry, 2013-07, Vol.34 (19), p.1697-1705

2013

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Charge transfer interaction in the effective fragment potential method

The Journal of chemical physics, 2006-06, Vol.124 (21), p.214108-214108-16

2006

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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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Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors

Nanoscale, 2011-01, Vol.3 (9), p.3635-3640

2011

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Random versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods

ACS omega, 2018-04, Vol.3 (4), p.4372-4377

2018

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On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion

Journal of the American Chemical Society, 1995-08, Vol.117 (31), p.8159-8170

1995

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Empirical corrections and pair interaction energies in the fragment molecular orbital method

Chemical physics letters, 2018-08, Vol.706, p.328-333

2018

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A graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values

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

Improving solvation energy predictions using the SMD solvation method and semiempirical electronic structure methods

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

Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions

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

Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry

Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods

FragIt: a tool to prepare input files for fragment based quantum chemical calculations

The effective fragment molecular orbital method for fragments connected by covalent bonds

Fully Integrated Effective Fragment Molecular Orbital Method

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

The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

Determinants of the Relative Reduction Potentials of Type-1 Copper Sites in Proteins

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

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

Charge transfer interaction in the effective fragment potential method

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

Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors

Random versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods

On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion

Empirical corrections and pair interaction energies in the fragment molecular orbital method

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