Jan H. Jensen

发表

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

Hui Li, Jan H. Jensen, Hui Li, 2004, J. Comput. Chem..

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Jan H. Jensen, Casper Steinmann, Mikael W. Ibsen, 2012, PloS one.

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

Jan H. Jensen, Lars A. Bratholm, Anders S. Larsen, 2015, PeerJ.

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

Jan H. Jensen, Gerald Monard, Ilke Ugur, 2014, J. Chem. Inf. Model..

My flipped classroom: what I did and how I did it

Jan H. Jensen, Jan H. Jensen, 2015 .

Applications of Parallel GAMESS

Mark S. Gordon, Michael W. Schmidt, Kim K. Baldridge, 1995 .

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

Gerhard Klebe, Nathan A. Baker, Jan H. Jensen, 2007, Nucleic Acids Res..

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

Jan H. Jensen, Casper Steinmann, Anders S. Christensen, 2014, PeerJ.

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

Hui Li, Jan H. Jensen, Pablo A. Molina, 2003, J. Comput. Chem..

Application driven software for chemistry

Teodor Rus, Jan H. Jensen, Donald Ephraim Curtis, 2008, 2008 IEEE International Conference on Electro/Information Technology.

Building a BioChemformatics Database

Jan H. Jensen, Thomas Hoeg-Jensen, Søren B. Padkjær, 2008, J. Chem. Inf. Model..

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

Kresten Lindorff-Larsen, Pengfei Tian, Jan H. Jensen, 2013, J. Comput. Chem..

Chemical Space Exploration: How Genetic Algorithms Find the Needle in the Haystack

Jan H. Jensen, Emilie S. Henault, Maria Harris Rasmussen, 2020 .

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

Hui Li, Mark S. Gordon, Jan H. Jensen, 2006, J. Comput. Chem..

General atomic and molecular electronic structure system

Mark S. Gordon, Michael W. Schmidt, Kim K. Baldridge, 1993, J. Comput. Chem..

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

Hui Li, Mark S. Gordon, Takeshi Nagata, 2009, J. Comput. Chem..

Fast and Automated Identification of Reactions with Low Barriers: The Decomposition of 3-Hydroperoxypropanal

Jan H. Jensen, Mads F. Madsen, Maria Harris Rasmussen, 2021, SciPost Chemistry.

Using a genetic algorithm to find molecules with good docking scores

Jan H. Jensen, Casper Steinmann, Casper Steinmann, 2021, PeerJ Physical Chemistry.

Molecular Modeling Basics

Jan H. Jensen, 2010 .

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

Hui Li, Jan H. Jensen, Hui Li, 2002 .

Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04156j

Jan H. Jensen, Jimmy C. Kromann, Morten Jørgensen, 2017, Chemical science.

BioFET-SIM Web Interface: Implementation and Two Applications

Jan H. Jensen, Luca De Vico, J. H. Jensen, 2012, PloS one.

Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method

Jan H. Jensen, Kazuo Kitaura, Dmitri G. Fedorov, 2009 .

The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties

Jan H. Jensen, Jimmy C. Kromann, Jimmy C Kromann, 2013 .

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

Jan H. Jensen, Jimmy C. Kromann, Morten Jørgensen, 2018 .

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

Jan H. Jensen, Casper Steinmann, Dmitri G. Fedorov, 2012, PloS one.

The Prediction of Protein pKa's Using QM/MM: The pKa of Lysine 55 in Turkey Ovomucoid Third Domain

Jan H. Jensen, Hui Li, J. H. Jensen, 2002 .

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

Jan H. Jensen, Pablo A. Molina, R. Steven Sikorski, 2003 .

Accurate Intraprotein Electrostatics Derived from First Principles: An Effective Fragment Potential Method Study of the Proton Affinities of Lysine 55 and Tyrosine 20 in Turkey Ovomucoid Third Domain

Jan H. Jensen, Visvaldas Kairys, J. H. Jensen, 2001 .

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

Kresten Lindorff-Larsen, Jan H. Jensen, Wouter Boomsma, 2013, PloS one.

Toward a General Theory of Hydrogen Bonding: The Short, Strong Hydrogen Bond [HOH···OH]-

Jan H. Jensen, Lynne C. Remer and, 2000 .

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

Jan H. Jensen, Laura L. Parker, A. Houk, 2006, Journal of the American Chemical Society.

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

Jan H. Jensen, Anders S. Christensen, S. Sauer, 2011, Journal of chemical theory and computation.

Effective Fragment Molecular Orbital Method

Jan H. Jensen, Casper Steinmann, 2017 .

Molecular quantum mechanics to biodynamics: Essential connections

Jan H. Jensen, J. H. Jensen, J. Rivail, 2006 .

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

Jan H. Jensen, Anders S. Christensen, Jimmy C. Kromann, 2018, ACS omega.

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

Jan H. Jensen, Anders S. Christensen, K. Mikkelsen, 2019, PeerJ Physical Chemistry.

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

Jan H. Jensen, Chresten R. Søndergaard, J. H. Jensen, 2011, Journal of chemical theory and computation.

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.

Jan H. Jensen, Chresten R. Søndergaard, J. H. Jensen, 2011, Journal of chemical theory and computation.

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

Jan H. Jensen, K. L. Martinez, J. Nygård, 2013, Nanotechnology.

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

Jan H. Jensen, J. H. Jensen, M. Brandbyge, 2011, Nanoscale.

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

Jan H. Jensen, Jan H Jensen, Simon P Webb, 2004, Journal of the American Chemical Society.

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

Jan H. Jensen, Pablo A. Molina, Melissa A Porter, 2006 .

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

Jan H. Jensen, M. H. Rasmussen, M. Rasmussen, 2020, PeerJ Physical Chemistry.

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

Jan H. Jensen, Chresten R. Søndergaard, J. H. Jensen, 2011, BMC Structural Biology.

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

Jan H. Jensen, J. H. Jensen, 2018, Chemical science.

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

Jan H. Jensen, Delphine Bas, D. Rogers, 2008, Proteins.

RegioML: Predicting the regioselectivity of electrophilic aromatic substitution reactions using machine learning

Jan H. Jensen, A. Göller, Nicolai Ree, 2021, Digital Discovery.

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

Jan H. Jensen, Jan H Jensen, J. H. Jensen, 2008, Proteins.

What the Heck?—Automated Regioselectivity Calculations of Palladium-Catalyzed Heck Reactions Using Quantum Chemistry

Jan H. Jensen, A. Göller, Nicolai Ree, 2022, ACS omega.

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

Jennifer D. Schuttlefield, Jan H. Jensen, J. Baltrusaitis, 2007, Physical chemistry chemical physics : PCCP.

Very fast empirical prediction and rationalization of protein pKa values

Jan H. Jensen, J. H. Jensen, A. D. Robertson, 2005, Proteins.

The determinants of carboxyl pKa values in turkey ovomucoid third domain

Jan H. Jensen, Hui Li, J. H. Jensen, 2004, Proteins.

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

Allen J. Flynn, Jan H. Jensen, J. H. Jensen, 2006, Biochemistry.

Indium arsenide nanowire field-effect transistors for pH and biological sensing

Jan H. Jensen, K. L. Martinez, P. Krogstrup, 2014 .

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

Jan H. Jensen, N. Powers, 2006, Journal of biomolecular NMR.

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

Jan H. Jensen, Anders S. Christensen, Jimmy C. Kromann, 2017, The Journal of chemical physics.

Glycine and the hydrogen bond: toward a model for solvation

Jan H. Jensen, J. H. Jensen, 1995 .

Virtual screening of norbornadiene-based molecular solar thermal energy storage systems using a genetic algorithm.

Jan H. Jensen, K. Mikkelsen, Nicolai Ree, 2021, The Journal of chemical physics.

A Neural Network Approach for Property Determination of Molecular Solar Cell Candidates.

Jan H. Jensen, K. Mikkelsen, R. B. Nielsen, 2022, The journal of physical chemistry. A.

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

Jan H. Jensen, J. H. Jensen, D. Fedorov, 2012, PloS one.

Prediction of pKa values using the PM6 semiempirical method

Jan H. Jensen, Jan H Jensen, Jimmy C. Kromann, 2016, PeerJ.

Calculation of Reduction Potential and pKa

Jan H. Jensen, J. H. Jensen, Hui Li, 2009 .

Spin excitations and quantum criticality in the quasi-one-dimensional Ising-like ferromagnet CoCl2·2D2O in a transverse field

Jan H. Jensen, G. Ehlers, S. R. Ahl, 2017 .

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

Jan H. Jensen, J. H. Jensen, 2015, Physical chemistry chemical physics : PCCP.

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

Jan H. Jensen, L. De Maria, M. Olsson, 2015, Computational and structural biotechnology journal.

Chapter 10 The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions

Jan H. Jensen, M. Gordon, Hui Li, 2007 .

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

Jan H. Jensen, G. Solomon, Mads Koerstz, 2018, The journal of physical chemistry letters.

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

Jan H. Jensen, J. H. Jensen, M. H. Rasmussen, 2020, PeerJ Physical Chemistry.

In Silico Prediction of Mutant HIV-1 Proteases Cleaving a Target Sequence

Jan H. Jensen, J. H. Jensen, J. Winther, 2014, PloS one.

Interface of the Polarizable Continuum Model of Solvation with Semi-Empirical Methods in the GAMESS Program

Jan H. Jensen, Anders S. Christensen, Casper Steinmann, 2013, PloS one.

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

Jan H. Jensen, J. H. Jensen, Hui Li, 2003 .

High Througput pKa Prediction Using Semi Empirical Methods

Jan H. Jensen, J. H. Jensen, 2015, 1512.00701.

Predicting binding free energies in solution

Jan H. Jensen, 2015, 1501.04428.

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

Jan H. Jensen, M. H. Rasmussen, M. Rasmussen, 2021, PeerJ Physical Chemistry.

Computational Evolution Of New Catalysts For The Morita-Baylis-Hillman Reaction.

Jan H. Jensen, Mogens Brøndsted Nielsen, Julius Seumer, 2023, Angewandte Chemie.

Toward a general theory of hydrogen bonding: A study of hydrogen bonds involving H2O and HF

Jan H. Jensen, J. H. Jensen, Ryan M. Minikis, 2000 .

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

Jan H. Jensen, Jimmy C. Kromann, J. H. Jensen, 2018, Chemical Physics Letters.

Towards a barrier height benchmark set for biologically relevant systems

Jan H. Jensen, Anders S. Christensen, Jimmy C. Kromann, 2016, PeerJ.

BioFET-SIM: A Tool for the Analysis and Prediction of Signal Changes in Nanowire-Based Field Effect Transistor Biosensors

Jan H. Jensen, M. Brandbyge, K. L. Martinez, 2013 .

Quantifying signal changes in nano-wire based biosensors.

Jan H. Jensen, D. Rogers, M. Brandbyge, 2011, Nanoscale.

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

Jan H. Jensen, J. H. Jensen, L. Olsen, 2017, The journal of physical chemistry. A.

Calculating pH and salt dependence of protein-protein binding.

Jan H. Jensen, Jan H Jensen, J. H. Jensen, 2008, Current pharmaceutical biotechnology.

Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases.

Jan H. Jensen, Jacob Kongsted, Ulf Ryde, 2007, Biochemistry.

Predicting pKa for proteins using COSMO-RS

Jan H. Jensen, Martin Peter Andersson, Jan Halborg Jensen, 2013, PeerJ.

Predicting pK a for proteins using

Jan H. Jensen, S. Stipp, C. Andersson, 2013 .

Prediction and rationalization of protein pKa values using QM and QM/MM methods.

Jan H. Jensen, Pablo A. Molina, J. H. Jensen, 2005, The journal of physical chemistry. A.

Bayesian inference of protein structure from chemical shift data

Jan H. Jensen, Thomas Hamelryck, Lars A. Bratholm, 2015, PeerJ.

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

Jan H. Jensen, J. H. Jensen, M. Naor, 2004, Proteins.

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

Jan H. Jensen, Jimmy C. Kromann, J. H. Jensen, 2018, The Journal of chemical physics.

Substituent Control of σ-Interference Effects in the Transmission of Saturated Molecules

Jan H. Jensen, G. Solomon, Mads Koerstz, 2021, ACS physical chemistry Au.

Predicting binding free energies in solution

Jan H. Jensen, 2015 .

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

Jan H. Jensen, M. Rasmussen, Diana S. Christensen, 2023, SciPost Chemistry.

Do machines dream of atoms? A quantitative molecular benchmark for explainable AI heatmaps

Jan H. Jensen, M. Rasmussen, Diana S. Christensen, 2022 .

In Silico Prediction of Mutant HIV-1 Proteases Cleaving a Target Sequence

Jan H. Jensen, J. Winther, M. Willemoës, 2014, PloS one.

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

Nathan A. Baker, Jan H. Jensen, Todd J. Dolinsky, 2007, Nucleic Acids Res..

Role of the virtual orbitals and HOMO-LUMO gap in mean-field approximations to the conductance of molecular junctions

Jan H. Jensen, K. Stokbro, H. Mera, 2008 .

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

Jan H. Jensen, G. Solomon, Mads Koerstz, 2018, The journal of physical chemistry letters.

Improved Selection of Rare Reactions in Template-Based Retrosynthesis Predictions

Jan H. Jensen, O. Engkvist, S. Genheden, 2021 .

Distributed under Creative Commons Cc-by 4.0 a Third-generation Dispersion and Third-generation Hydrogen Bonding Corrected Pm6 Method: Pm6-d3h+

Jan H. Jensen, Anders S. Christensen, M. Korth, 2022 .

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

Jan H. Jensen, Lars A. Bratholm, J. H. Jensen, 2016, Chemical science.

Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods.

Jan H. Jensen, Casper Steinmann, Jan H Jensen, 2010, The journal of physical chemistry. A.

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

Jan H. Jensen, Kazuo Kitaura, Jan H Jensen, 2008, The journal of physical chemistry. A.