Biochemical molecules studied by theoretical methods
- Ligand binding
- The relation between structure and function of proteins
- Enzyme mechanisms
- The influence of the protein on bound metals, ligands and chromophores
- Nature's design of proteins (Why was that metal or amino acid selected?)
- QM/MM methods
- Combination of QM methods and experimental methods: e.g. X-ray crystallography, NMR, EXAFS, neutron crystallography.
- P. Mikulskis, S. Genheden, U. Ryde (2014) "Large-scale test of free-energy simulation estimates of protein-ligand binding affinities", J. Chem. Inf. Model., 54, 2794-2806; DOI: 10.1021/ci5004027.
- P. Mikulskis, D. Cioloboc, M. Andrejic, S. Khare, J. Brorsson, S. Genheden, R. A. Mata, P. Söderhjelm, U. Ryde (2014) "Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies", J. Comp.-Aided Mol. Design, 28, 375-400; DOI: 10.1007/s10822-014-9739-x.
- L. Hu, P. Söderhjelm, U. Ryde "Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations" J. Chem. Theory Comput. 2013, 9, 640-649; DOI 10.1021/ct3005003.
- S. Genheden, P. Mikulskis, L. Hu, J. Kongsted, P. Söderhjelm, U. Ryde "Accurate predictions of non-polar solvation free energies require explicit consideration of binding site hydration", J. Am. Chem. Soc., 2011, 133, 13081-13092; DOI 10.1021/ja202972m.
- P. Söderhjelm, C. Husberg, A. Strambi, M. Olivucci, U. Ryde (2009) "Protein influence on electronic spectra modelled by multipoles and polarisabilities", J. Chem. Theory Comput. 5, 649-658; DOI: 10.1021/ct700347h.
- P. Söderhjelm, U. Ryde (2009) "How accurate can a force field become? - A polarizable multipole model combined with fragment-wise quantum-mechanical calculations" J. Phys. Chem. A, 113, 617-627; DOI: 10.1021/jp8073514.
- U. Ryde, L. Olsen & K. Nilsson (2002) "Quantum chemical geometry optimisations in proteins using crystallographic raw data", J. Comp. Chem., 23, 1058-1070. DOI 10.1002/jcc.10093.
- T. H. Rod & U. Ryde (2005) "Free energy barriers at the density functional theory level: methyl transfer catalyzed by catechol O-methyltransferase", J. Chem. Theory Comput., 1, 1240-1251; DOI:10.1021/ct0501102.
- U. Ryde, M. H. M. Olsson, K. Pierloot & B. O. Roos (1996) "The cupric geometry of blue copper proteins is not strained". J. Mol. Biol. 261, 586-596. DOI: 10.1006/jmbi.1996.0484
with references to my list of publications
- Computational estimates for ligand-binding using FEP [153,196,200], MM/PB(GB)SA [90,117,134,141,147,172,173,174,179,185,195,204], LIE [164,174], QM methods [114,125,169,196,199,207]; non-polar solvation [145,156]; enthalpy–entropy compensation 
- Mechanisms of Mo-enzymes [128,184,198,201,205]
- Entropies from MD simulations and NMR experiments [143,171,191]
- Hydrogenases: NiFe [87,194], FeFe [99,100,112,122,138,151,152,155,159,161,162], Fe [190,203]
- Galectin 3 [126,144,167]
- Superoxide dismuatases [83,84,123,165]
- Multi-copper oxidases [77,92,140,148,163,175,180,206]
- QM/MM methods [20,40,51,60,129,150,181,188]
- QM/MM free energies (QTCP) [75,78,82,101,106,111,177,206]
- Parameterisation of MM methods: charges for MM calculations [25,45,120,168]; polarisabilities ; metal sites ; NEMO [86,97,104]; PMISP [118,125]; Solvation methods 
- Cytochrome P450 [64,89,98,107,110,116,176]
- Influence of protein on spectroscopic properties [121,149]
- Metallo beta-lactamase [54,69]
- Porphyrin metallation and ferrochelatase [53,56,66,72,80,131]
- Combination of QM methods with X-ray crystallography [47,50,58,62,67,68,74,80,81,94,108,113,136,192], NMR  and EXAFS [18,91,96,202]
- Coenzyme B12 proteins [46,55,59,61,76,119,160]
- Electron-transfer proteins (iron-sulphur, cytochromes, and CuA) [42-44]
- Carboxylate shifts in zinc proteins 
- Discrimination between O2 and CO by myoglobin [31,48]; binding of O2 to haem proteins [65,70]
- FeS clusters [105,115,133,142]
- Porphyrin proteins [43,55,57,64,71,79]
- Blue copper proteins [21,22,26-30,32,34,35,38-41,43,44,49,63]
- Interpretation of PAC experiments [18,24,33]
- Alcohol dehydrogenase [15-17,19,20,24,67]
- Oscillations in biochemical systems [7,11-14]
- The Calvin cycle [1-6,8-10]
- Rubus Sect. Corylifolii [132,137,146,166]
- blue copper proteins, e.g. plastocyanin, nitrite reducates, and azurin
- Mo enzymes (DMSO reductase, sulfite oxidase, xanthine oxidase)
- porphyrin proteins, e.g. myoglobin, Fe/Mg-chelatase, cytochrome P450, cytochromes, peroxidases, catalases, vitamin B12 and coenzyme F430 enzymes
- catechol O-methyl transferase
- iron-sulphur clusters
- superoxide dismuatases (Cu/Zn, Fe, Mn, or Ni)
- NiFe, FeFe, and Fe hydrogenases
- multi-copper oxidases
- zinc enzymes, e.g. alcohol dehydrogenase, metallo-beta-lactamase, carbanhydrase, thermolysin, and carboxypeptidase
- ab initio quantum chemistry (HF to CASPT2)
- Local LCCSD(T0) methods
- density functional theory, including B3LYP, BP86, PBE, and TPSS
- molecular dynamics
- molecular mechanics
- free energy perturbation
- combined quantum chemical and classical methods (QM/MM)
- combined quantum chemical and crystallographic refinement methods (Quantum refinement)
- QM/MM combined with NMR refinement
- QM and QM/MM combined with EXAFS refinement
- QM/MM free energy methods (QTCP)
- Accurate force fields, parametrisation
We develop methods to be used in simulations of proteins. Here are some of them.
- ComQum, a combined quantum chemical and molecular mechanical (QM/MM) geometry optimisation program.
- ComQum-X , a combined quantum chemical and crystallographic refinement program
- ComQum-N, a combined quantum chemical and NMR program
- ComQum-EXAFS, a combined quantum chemical and EXAFS program
- Chargefit, a program to fit atomic charges to electrostatic moments or potential, e.g. the methods CHELMO and CHELP-BOW.
- QTCP, a method for high-level QM/MM free energies
- Accurate parametrisations (PON)
More about software.
We also have done some parameterisation of protein ligands. These are most of them. Please, contact me if you are interested in the parameters.
- A four- or five-coordinate zinc ion with His, Cys, water, and hydroxide ligands. (to be used for alcohol dehydrogenase)
- Cu(II) ions with His, Cys, Met, and water ligands; (to be used for blue copper sites, the type 2 copper site in nitrite reductase, and Cu-substituted alcohol dehydrogenase)
- Negatively charged Cys
- NADH, NAD+, NADPH, and NADP+
- Neutral Arg and Lys
- Numerous protein ligands
Current group members
- Lili Cao (PhD student 2016-2020)
- Octav Caldararu (PhD student 2015-2019)
- Majda Misini Ignjatovic (PhD student 2015-2019)
- Geng Dong (PhD student 2014-2018)
- Martin A. Olsson (PhD student 2014-2018)
- Francesco Manzoni (PhD student, shared with Derek Logan, Biochemistry, 2013-2017)
Former group members
- Dr. Paulius Mikulskis (PhD student 2011-2015); currently in Nottingham.
- Dr. Jilai Li (Postdoc 2011-2012), currently in Berlin.
- Dr. Samuel Genheden (PhD student 2008-2012), currently in Göteborg.
- Dr. Marie-Céline van Severen (Postdoc 2009-2011).
- LiHong Hu (Postdoc 2010-2011).
- Dr. Jimmy Heimdal (PhD student 2006-2010), currently at Max in Lund.
- Dr. Maryam Farrokhnia (Postdoc 2009).
- Dr. Pär Söderhjelm (PhD student 2003-2008), currently at Biophysical Chemistry, Lund.
- Dr. Jacob Kongsted (Postdoc 2007-2008), currently in Odense.
- Dr. Patrik Rydberg (PhD student 2002-2007), deseased in 2013.
- Dr. Marcus Kaukonen (Postdoc 2006-2008), currently in Helsinki.
- Kambiz Katebzadeh (Project worker 2005-2006).
- Aaron Weis (Diploma worker 2005).
- Dr. Thomas H. Rod (Postdoc 2003-2005), currently at ESS in Copenhagen.
- Dr. Ya-Wen Hsiao (Postdoc 2003-2005).
- Dr. Yong Shen (Postdoc 2003-2004).
- Dr. Kasper Planeta Jensen/Kepp (PhD student 2001-2004), currently at DTU.
- Dr. Lubomir Rulisek (Postdoc 2002-2004), currently at UOCHB AV CR in Prague, Czech Republic.
- Dr. Kristina Nilsson (PhD student 1998-2003), "Quantum chemical interpretations of protein crystal structures", Lund, December 12, 2003.
- Dr. Torben Rasmussen (Postdoc 2002-2003), currently at Linköping supercomputer centre.
- Dr. Emma Sigfridsson (PhD student 1997-2001), now Emma Evertsson, "Theoretical studies of porphyrin proteins", Lund, September 21, 2001. Currently at AstraZeneca, Mölndal.
- Dr. Mats Olsson (PhD student 1995-2000), "Theoretical studies of blue copper proteins", Lund, March 3, 2000. Post doc in A. Warshel's group, University of South California. Currently in Copenhagen.
- Jan O. A. De Kerpel (PhD student in Leuven 1995-1999), "Molecular and electronic modeling of blue copper proteins", Leuven Jan 1999. Currently at Devgen, Belgium.
- Dr. Conrad Newton (Postdoc 1998-1999).
- Dr. Antonio Carlos Borin (Postdoc 1996-1997), currently in Sao Paolo, Brazil.
- Dr. Lars Hemmingsen (Postdoc 1996), currently at DTU, Lyngby, Denmark.
Degrees and Titles
- Master of Scence in Chemistry (Dec. 12, 1986)
- Doctor of Philosophy in Biochemistry (Oct. 9, 1991)
- Docent in Theoretical Chemistry (Mar. 20, 1996)
- Assistant Professor (July 1, 1992; Forskarassistent)
- Associate Professor (Feb. 1, 2000; Lektor)
- Advisor for PhD students at the Chemical Section in Lund university (May 1, 2000- Dec. 12 2001; studierektor)
- Senior research position in bioinorganic chemistry, Lund university (July 1, 2001-2007; Särskild forskare)
- Professor in Theoretical Chemistry (Mar. 1, 2004)
- Music (I play the piano, church organ, and sing in choirs)
- Botany (plants, especially blackberries, and fungi)