53 citations · 294 across the 16 of their papers we have counts for
16 papers
Empirical corrections and pair interaction energies in the fragment molecular orbital method
Dmitri G. Fedorov, Jimmy C. Kromann, Jan H. Jensen
The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to…
Guiding Chemical Synthesis: Computational Prediction of the Regioselectivity of CH Functionalization
Jan H. Jensen
We will develop a computational method (RegioSQM) for predicting the regioselectivity of CH functionalization reactions that can be used by synthetic chemists who are not experts i…
High Througput pKa Prediction Using Semi Empirical Methods
Jan H. Jensen
A large proportion of organic molecules relevant to medicine and biotechnology contain one or more ionizable groups, which means that fundamental physical and chemical properties (…
Predicting binding free energies in solution
Jan H. Jensen
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while oth…
In silico prediction of mutant HIV-1 proteases cleaving a target sequence
Jan H. Jensen, Martin Willemoës, Jakob R. Winther +1
HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied…
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
Martin R. Hediger, Casper Steinmann, Luca De Vico +1
We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on…
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Anders S. Christensen, Troels E. Linnet, Mikael Borg +4
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that det…
Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method
Anders S. Christensen, Casper Steinmann, Dmitri G. Fedorov +1
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the…
Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program
Casper Steinmann, Kristoffer L. Blædel, Anders S. Christensen +1
An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem…
The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties
Jan H. Jensen, Jimmy C. Kromann
A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can…
Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry
Casper Steinmann, Dmitri G. Fedorov, Jan H. Jensen
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarizat…
In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB
Martin R. Hediger, Luca De Vico, Julie B. Rannes +4
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., arXiv:1203.2950) is benchmarked against experimentally measured amid…
FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations
Casper Steinmann, Mikael W. Ibsen, Anne S. Hansen +1
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research.…
BioFET-SIM Web Interface: Implementation and Two Applications
Martin R. Hediger, Jan H. Jensen, Luca De Vico
We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustratio…
A Computational Methodology to Screen Activities of Enzyme Variants
Martin R. Hediger, Luca De Vico, Allan Svendsen +2
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction…
The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
Casper Steinmann, Dmitri G. Fedorov, Jan H. Jensen
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab in…