List of works - Jan H. Jensen

A computational method for the systematic screening of reaction barriers in enzymes: searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate

scientific article published on 23 July 2013

A computational methodology to screen activities of enzyme variants

scientific article (publication date: 2012)

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

scientific article published on 11 February 2019

A planar tetracoordinate carbon and unusual bonding in an organodimetallic propynylidene complex arising from double C-H activation of an allene ligand

scientific article

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

scientific article published on 19 June 2014

Bayesian inference of protein structure from chemical shift data.

scientific article

BioFET-SIM web interface: implementation and two applications

scientific article published on 8 October 2012

Charge transfer interaction in the effective fragment potential method

scientific article published on 01 June 2006

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

Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

scientific article

Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface

article by Hui Li et al published 1 March 2003 in Theoretical Chemistry Accounts

Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins.

scientific article

Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method

scientific article

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

scientific article published on 09 June 2011

Determinants of cysteine pKa values in creatine kinase and alpha1-antitrypsin

scientific article published in December 2004

Determinants of the relative reduction potentials of type-1 copper sites in proteins

scientific article

Do machines dream of atoms? Crippen's logP as a quantitative molecular benchmark for explainable AI heatmaps

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

scientific article published on 9 April 2015

Effective Fragment Method for Modeling Intermolecular Hydrogen-Bonding Effects on Quantum Mechanical Calculations

scientific article published on 5 May 1994

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

scientific article published on 01 August 2010

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

scientific article published on 21 December 2012

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

article

Exploring the role of the active site cysteine in human muscle creatine kinase

scientific article

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 Fe2O3and Al2O3

scientific article published on 01 June 2006

FTIR spectroscopy combined with quantum chemical calculations to investigate adsorbed nitrate on aluminium oxide surfaces in the presence and absence of co-adsorbed water

scientific article published in 2007

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

scientific article published on 13 November 2017

Fast and automated identification of reactions with low barriers: the decomposition of 3-hydroperoxypropanal

scientific article published in October 2021

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

scientific article

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

scientific article

Fully Integrated Effective Fragment Molecular Orbital Method.

scientific article published on 12 April 2013

General atomic and molecular electronic structure system

article

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

scientific article

Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method

scientific article

Hydride transfer versus hydrogen radical transfer in thymidylate synthase.

scientific article published on May 2006

Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of α-helices

scientific article published on 01 May 2006

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

scientific article published on 9 June 2011

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

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation

scientific article published in September 2004

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

scientific article (publication date: 2014)

In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB.

scientific article published on 29 August 2013

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program.

scientific article

Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

scientific article

Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations

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

scientific article

Molecular quantum mechanics to biodynamics: Essential connections

scholarly article by Michael E. Colvin et al published May 2006 in Computational and Theoretical Chemistry

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

scientific article

Partial Hessian vibrational analysis: the localization of the molecular vibrational energy and entropy

article

Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods

scientific article published on 01 May 2015

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

scientific article

Predicting pKa for proteins using COSMO-RS.

scientific article published on 31 October 2013

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

scientific article published on 5 January 2017

Prediction of pKa values using the PM6 semiempirical method.

scientific article published on 11 August 2016

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

scientific article

Protein structure refinement using a quantum mechanics-based chemical shielding predictor

scientific article

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

scientific article (publication date: 2013)

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

scientific article published on 01 April 2008

Quantifying signal changes in nano-wire based biosensors

scientific article published on 20 December 2010

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

scientific article published on 20 April 2018

Rationalization of the difference in lifetime of two covalent sialosyl-enzyme intermediates of Trypanosoma rangeli sialidase

scientific article

Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pKa’s

scientific article published on 13 August 2014

Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

scientific article

Splicing I: Using mixed basis sets inab initio calculations

Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2

scientific article published on 01 July 2007

Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 1.

scientific article published in July 2007

The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators

scientific article published on 30 November 2018

The determinants of carboxyl pKa values in turkey ovomucoid third domain

scientific article published in May 2004

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

scientific article

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

article

Towards a barrier height benchmark set for biologically relevant systems.

scientific article

Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets

scientific article published on 18 December 2023

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

scientific article

List of works by Jan H. Jensen

A computational method for the systematic screening of reaction barriers in enzymes: searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate

A computational methodology to screen activities of enzyme variants

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

A planar tetracoordinate carbon and unusual bonding in an organodimetallic propynylidene complex arising from double C-H activation of an allene ligand

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

Bayesian inference of protein structure from chemical shift data.

BioFET-SIM web interface: implementation and two applications

Charge transfer interaction in the effective fragment potential method

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

Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface

Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins.

Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

Determinants of cysteine pKa values in creatine kinase and alpha1-antitrypsin

Determinants of the relative reduction potentials of type-1 copper sites in proteins

Do machines dream of atoms? Crippen's logP as a quantitative molecular benchmark for explainable AI heatmaps

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

Effective Fragment Method for Modeling Intermolecular Hydrogen-Bonding Effects on Quantum Mechanical Calculations

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

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

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

Exploring the role of the active site cysteine in human muscle creatine kinase

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 Fe2O3and Al2O3

FTIR spectroscopy combined with quantum chemical calculations to investigate adsorbed nitrate on aluminium oxide surfaces in the presence and absence of co-adsorbed water

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

Fast and automated identification of reactions with low barriers: the decomposition of 3-hydroperoxypropanal

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

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

Fully Integrated Effective Fragment Molecular Orbital Method.

General atomic and molecular electronic structure system

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

Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method

Hydride transfer versus hydrogen radical transfer in thymidylate synthase.

Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of α-helices

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

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

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation

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

In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB.

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program.

Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations

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

Molecular quantum mechanics to biodynamics: Essential connections

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

Partial Hessian vibrational analysis: the localization of the molecular vibrational energy and entropy

Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods

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

Predicting pKa for proteins using COSMO-RS.

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

Prediction of pKa values using the PM6 semiempirical method.

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

Protein structure refinement using a quantum mechanics-based chemical shielding predictor

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

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

Quantifying signal changes in nano-wire based biosensors

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

Rationalization of the difference in lifetime of two covalent sialosyl-enzyme intermediates of Trypanosoma rangeli sialidase

Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pKa’s

Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

Splicing I: Using mixed basis sets inab initio calculations

Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2

Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 1.

The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators

The determinants of carboxyl pKa values in turkey ovomucoid third domain

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

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Towards a barrier height benchmark set for biologically relevant systems.

Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets

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

Which method is more accurate? or errors have error bars

Which method is more accurate? or errors have error bars