General atomic and molecular electronic structure system. - Michael W. Schmidt; Kim K. Baldridge; Jerry A. Boatz; Steven T. Elbert; Mark S. Gordon; Jan H. Jensen; Shiro Koseki; Nikita Matsunaga; Kiet A. Nguyen; Shujun Su; Theresa L. Windus; Michel Dupuis; et al. (J. Comput. Chem., 1993)

Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations. - Pablo A. Molina; Hui Li; Jan H. Jensen (J. Comput. Chem., 2003)

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 (J. Comput. Chem., 2004)

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). - Dmitri G. Fedorov; Kazuo Kitaura; Hui Li; Jan H. Jensen; Mark S. Gordon (J. Comput. Chem., 2006)

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. - Todd J. Dolinsky; Paul Czodrowski; Hui Li; Jens Erik Nielsen; Jan H. Jensen; Gerhard Klebe; Nathan A. Baker (Nucleic Acids Res., 2007)

Application driven software for chemistry. - Donald Ephraim Curtis; Teodor Rus; Jan H. Jensen (EIT, 2008)

Building a BioChemformatics Database. - Jan H. Jensen; Thomas Hoeg-Jensen; Søren B. Padkjær (J. Chem. Inf. Model., 2008)

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. - Hui Li; Dmitri G. Fedorov; Takeshi Nagata; Kazuo Kitaura; Jan H. Jensen; Mark S. Gordon (J. Comput. Chem., 2010)

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations - Casper Steinmann; Mikael W. Ibsen; Anne S. Hansen; Jan H. Jensen (CoRR, 2012)

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. - Wouter Boomsma; Jes Frellsen; Tim Harder; Sandro Bottaro; Kristoffer E. Johansson; Pengfei Tian; Kasper Stovgaard; Christian Andreetta; Simon Olsson; Jan B. Valentin; Lubomir D. Antonov; Anders S. Christensen; et al. (J. Comput. Chem., 2013)

Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pKa's. - Ilke Ugur; Antoine Marion; Stéphane Parant; Jan H. Jensen; Gerald Monard (J. Chem. Inf. Model., 2014)

pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides. - Esben Jannik Bjerrum; Jan H. Jensen; Jakob L. Tolborg (J. Chem. Inf. Model., 2017)

RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions. - Nicolai Ree; Andreas H. Göller; Jan H. Jensen (J. Cheminformatics, 2021)

Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets. - Maria H. Rasmussen; Chenru Duan; Heather J. Kulik; Jan H. Jensen (J. Cheminformatics, 2023)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

SMILES all around: structure to SMILES conversion for transition metal complexes. - Maria H. Rasmussen; Magnus Strandgaard; Julius Seumer; Laura K. Hemmingsen; Angelo Frei; David Balcells; Jan H. Jensen (J. Cheminformatics, 2025)