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QM Calculations for Enzyme Activity Screening

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QM Calculations for Enzyme Activity Screening

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  • Host: GitHub
  • Owner: mzhKU
  • Language: TeX
  • Default Branch: master
  • Size: 16.8 MB
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Created almost 12 years ago · Last pushed over 11 years ago
Metadata Files
Readme Citation

readme.txt

QM Calculations for Enzyme Activity Screening
---------------------------------------------
Martin Hediger

Style Guide (recommended)
---------------------------------------------
- Sentences on separate lines
- Spell in full abbreviations if first word of
  sentence, such as Eq./Eqs., Fig./Figs., Ref./Refs.
  or Sec./Secs.
- Italize Latin words
- Italize using \textit{}

File Guide
---------------------------------------------
000-main.tex: Main PDF output file
010-main.tex: Chapter file
999-*.tex   : Backup files
040-*.*     : Figures
pages.txt:  : Links collection file

Compilation
---------------------------------------------
(1) pdflatex 000-main
(2) pdflatex 000-main
(3) bibtex   000-main
(5) pdflatex 000-main

Useful git commands
---------------------------------------------
Check if pull required:
git fetch -v --dry-run
git remote -v update

Check commits which are not yet pushed to remote:
git log --branches --not --remotes

Only most recent:
git log --branches --not --remotes --simplify-by-decoration --decorate --oneline

PYMOL Commands for ray tracing
---------------------------------------------
See: http://cupnet.net/ambient-occlusion-pymol/
fetch 1BTA
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
remove solvent
as spheres
util.cbaw
bg white
set light_count,10
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
ray 1200, 1200

Notes 30.05.14
---------------------------------------------
Conclusions:
Outlook? Summary? How to evolve the field?
And when we look back at the two companies from the beginning?
Requirements: Structure (only) required if *this* method should be used.

Owner

  • Name: Martin Hediger
  • Login: mzhKU
  • Kind: user

Citation (citations.bib)

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publisher={The Royal Society of Chemistry},
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url={http://dx.doi.org/10.1039/C1CC10865D},
abstract={Based on molecular modelling{,} the enzyme Candida antarctica lipase B was redesigned as a catalyst for the ring opening polymerization of d{,}d-lactide. Two mutants with 90-fold increased activity as compared to the wild-type enzyme were created. In a preparative synthesis of poly(d{,}d-lactide) the mutants greatly improved the rate and the degree of polymerization.}
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year = {2011},
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@article{hu2008free,
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  author={Hu, H. and Yang, W.},
  journal={Annu. Rev. Phys. Chem.},
  volume={59},
  pages={573--601},
  year={2008},
  publisher={Annual Reviews}
}
@article{von1993rational,
  title={Rational design of potent sialidase-based inhibitors of influenza virus replication},
  author={Von Itzstein, M. and Wu, W.Y. and Kok, G.B. and Pegg, M.S. and Dyason, J.C. and Jin, B. and Van Phan, T. and Smythe, M.L. and White, H.F. and Oliver, S.W. and others},
  journal={Nature},
  volume={363},
  number={6428},
  pages={418--423},
  year={1993},
  publisher={Nature Publishing Group}
}

@article{schames2004discovery,
  title={Discovery of a novel binding trench in HIV integrase},
  author={Schames, J.R. and Henchman, R.H. and Siegel, J.S. and Sotriffer, C.A. and Ni, H. and McCammon, J.A.},
  journal={Journal of medicinal chemistry},
  volume={47},
  number={8},
  pages={1879--1881},
  year={2004},
  publisher={ACS Publications}
}

@article{benkovic2003perspective,
  title={A perspective on enzyme catalysis},
  author={Benkovic, S.J. and Hammes-Schiffer, S.},
  journal={Science},
  volume={301},
  number={5637},
  pages={1196--1202},
  year={2003},
  publisher={American Association for the Advancement of Science}
}

@article{vellard2003enzyme,
  title={The enzyme as drug: application of enzymes as pharmaceuticals},
  author={Vellard, M.},
  journal={Current opinion in biotechnology},
  volume={14},
  number={4},
  pages={444--450},
  year={2003},
  publisher={Elsevier}
}
@article{margolin1993enzymes,
  title={Enzymes in the synthesis of chiral drugs},
  author={Margolin, A.L.},
  journal={Enzyme and microbial technology},
  volume={15},
  number={4},
  pages={266--280},
  year={1993},
  publisher={Elsevier}
}

@article{beilen2002enzyme,
  title={Enzyme technology: an overview},
  author={Beilen, J.B. and Li, Z.},
  journal={Current Opinion in Biotechnology},
  volume={13},
  number={4},
  pages={338--344},
  year={2002},
  publisher={Elsevier}
}
@article{sidhu1999sugar,
  title={Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase},
  author={Sidhu, G. and Withers, S.G. and Nguyen, N.T. and McIntosh, L.P. and Ziser, L. and Brayer, G.D.},
  journal={Biochemistry},
  volume={38},
  number={17},
  pages={5346--5354},
  year={1999},
  publisher={ACS Publications}
}

@article{klamt1993cosmo,
  title={COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient},
  author={Klamt, A. and Sch{\"u}{\"u}rmann, G.},
  journal={J. Chem. Soc., Perkin Trans. 2},
  number={5},
  pages={799--805},
  year={1993},
  publisher={The Royal Society of Chemistry}
}
@article{fedorov2004second,
  title={Second order M{\o}ller-Plesset perturbation theory based upon the fragment molecular orbital method},
  author={Fedorov, Dmitri G and Kitaura, Kazuo},
  journal={The Journal of Chemical Physics},
  volume={121},
  number={6},
  pages={2483--2490},
  year={2004},
  publisher={American Institute of Physics}
}
@article{steinmann2012mapping,
  title={Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry},
  author={Steinmann, Casper and Fedorov, Dmitri G and Jensen, Jan H},
  journal={arXiv preprint arXiv:1212.6172},
  year={2012}
}
@article{steinmann2012fragit,
  title={FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations},
  author={Steinmann, Casper and Ibsen, Mikael W and Hansen, Anne S and Jensen, Jan H},
  journal={PLOS ONE},
  volume={7},
  number={9},
  pages={e44480},
  year={2012},
  publisher={Public Library of Science}
}
@article{ct100578z,
author = {Olsson, Mats H. M. and S{\o}ndergaard, Chresten R. and Rostkowski, Michal and Jensen, Jan H.},
title = {PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions},
journal = {Journal of Chemical Theory and Computation},
volume = {7},
number = {2},
pages = {525-537},
year = {2011},
doi = {10.1021/ct100578z},

URL = {http://pubs.acs.org/doi/abs/10.1021/ct100578z},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct100578z}
}
@article{jiang2008novo,
  title={De novo computational design of retro-aldol enzymes},
  author={Jiang, Lin and Althoff, Eric A and Clemente, Fernando R and Doyle, Lindsey and R{\"o}thlisberger, Daniela and Zanghellini, Alexandre and Gallaher, Jasmine L and Betker, Jamie L and Tanaka, Fujie and Barbas, Carlos F and others},
  journal={Science},
  volume={319},
  number={5868},
  pages={1387--1391},
  year={2008},
  publisher={American Association for the Advancement of Science}
}
@article{Gordon2012,
author = {Gordon, Sydney R. and Stanley, Elizabeth J. and Wolf, Sarah and Toland, Angus and Wu, Sean J. and Hadidi, Daniel and Mills, Jeremy H. and Baker, David and Pultz, Ingrid Swanson and Siegel, Justin B.},
title = {{Computational Design of an $\alpha$-Gliadin Peptidase}},
journal = {Journal of the American Chemical Society},
volume = {134},
number = {50},
pages = {20513-20520},
year = {2012},
doi = {10.1021/ja3094795}
}
@article{Siegel2010,
author = {Siegel, Justin B. and Zanghellini, Alexandre and Lovick, Helena M. and Kiss, Gert and Lambert, Abigail R. and St.Clair, Jennifer L. and Gallaher, Jasmine L. and Hilvert, Donald and Gelb, Michael H. and Stoddard, Barry L. and Houk, Kendall N. and Michael, Forrest E. and Baker, David}, 
title = {Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction},
volume = {329}, 
number = {5989}, 
pages = {309-313}, 
year = {2010}, 
doi = {10.1126/science.1190239}, 
abstract ={The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.}, 
URL = {http://www.sciencemag.org/content/329/5989/309.abstract}, 
eprint = {http://www.sciencemag.org/content/329/5989/309.full.pdf}, 
journal = {Science} 
}

@article{Hariharan1973,
   author = {Hariharan, P. C. and Pople, J. A.},
   title = "{The influence of polarization functions on molecular orbital hydrogenation energies}",
   journal = {Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)},
   publisher = {Springer Berlin / Heidelberg},
   issn = {1432-881X},
   keyword = {Chemistry and Materials Science},
   pages = {213-222},
   volume = {28},
   issue = {3},
   url = {http://dx.doi.org/10.1007/BF00533485},
   note = {10.1007/BF00533485},
   abstract = {Polarization functions are added in two steps to a split-valence extended gaussian basis set: d -type gaussians on the first row atoms C. N, O and F and p -type gaussians on hydrogen. The same d -exponent of 0.8 is found to be satisfactory for these four atoms and the hydrogen p -exponent of 1.1 is adequate in their hydrides. The energy lowering due to d functions is found to depend on the local symmetry around the heavy atom. For the particular basis used, the energy lowerings due to d functions for various environments around the heavy atom are tabulated. These bases are then applied to a set of molecules containing up to two heavy atoms to obtain their LCAO-MO-SCF energies. The mean absolute deviation between theory and experiment (where available) for heats of hydrogenation of closed shell species with two non-hydrogen atoms is 4 kcal/mole for the basis set with full polarization. Estimates of hydrogenation energy errors at the Hartree-Fock limit, based on available calculations, are given.},
   year = {1973}
}

@article{Tomasi2005,
author = {Tomasi, Jacopo and Mennucci, Benedetta and Cammi, Roberto},
title = "{Quantum Mechanical Continuum Solvation Models}",
journal = {Chemical Reviews},
volume = {105},
number = {8},
pages = {2999-3094},
year = {2005},
doi = {10.1021/cr9904009},
URL = {http://pubs.acs.org/doi/abs/10.1021/cr9904009},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/cr9904009}
}

@article{fmo2002,
title = "{Fragment molecular orbital method: use of approximate electrostatic potential}",
journal = "Chemical Physics Letters",
volume = "351",
number = "5--6",
pages = "475 - 480",
year = "2002",
note = "",
issn = "0009-2614",
doi = "10.1016/S0009-2614(01)01416-6",
url = "http://www.sciencedirect.com/science/article/pii/S0009261401014166",
author = "Tatsuya Nakano and Tsuguchika Kaminuma and Toshiyuki Sato and Kaori Fukuzawa and Yutaka Akiyama and Masami Uebayasi and Kazuo Kitaura",
abstract = "Recently, we have proposed the fragment molecular orbital (FMO) method; an approximate MO method for calculating large molecules such as proteins. The method has been shown to reproduce ab initio total energies and geometries of molecules in good accuracy. The most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation. Numerical calculations on several polypeptides revealed that the approximations brought no significant loss of accuracy in the total energy of molecules and were of practical use."
}

@article{fmo2007,
author = {Fedorov, Dmitri G. and Kitaura, Kazuo},
title = "{Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method}",
journal = {The Journal of Physical Chemistry A},
volume = {111},
number = {30},
pages = {6904-6914},
year = {2007},
doi = {10.1021/jp0716740},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp0716740},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0716740},
abstract = { Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (α-helix, β-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB:  1L2Y) are analyzed using PIEDA. }
}

@article{Fedorov2006,
author = {Fedorov, Dmitri G. and Kitaura, Kazuo and Li, Hui and Jensen, Jan H. and Gordon, Mark S.},
title = {{The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)}},
journal = {Journal of Computational Chemistry},
volume = {27},
number = {8},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1096-987X},
url = {http://dx.doi.org/10.1002/jcc.20406},
doi = {10.1002/jcc.20406},
pages = {976--985},
keywords = {fragment molecular orbital, FMO, polarizable continuum model, PCM, GAMESS, parallel, GDDI, protein},
year = {2006},
abstract = {The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)–solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including α-helices and β-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of α-helices and β-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues, and the solvation energy and computational efficiency are discussed. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 976–985, 2006},
}

@article{Francl1982,
author = {Michelle M. Francl and William J. Pietro and Warren J. Hehre and J. Stephen Binkley and Mark S. Gordon and Douglas J. DeFrees and John A. Pople},
collaboration = {},
title = "{Self-consistent molecular orbital methods. {XXIII}. {A} polarization-type basis set for second-row elements}",
publisher = {AIP},
year = {1982},
journal = {The Journal of Chemical Physics},
volume = {77},
number = {7},
pages = {3654-3665},
keywords = {MOLECULAR ORBITAL METHOD; SELFCONSISTENT FIELD; WAVE FUNCTIONS; LITHIUM; BERYLLIUM; BORON; CARBON; NITROGEN; OXYGEN; FLUORINE; NEON; ELECTRONIC STRUCTURE; HYDRIDES; MOLECULAR STRUCTURE},
url = {http://link.aip.org/link/?JCP/77/3654/1},
doi = {10.1063/1.444267}
}

@article{fedorov2011geometry,
author = {Fedorov, Dmitri G. and Alexeev, Yuri and Kitaura, Kazuo},
title = {Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method},
journal = {The Journal of Physical Chemistry Letters},
volume = {2},
number = {4},
pages = {282-288},
year = {2011},
doi = {10.1021/jz1016894},

URL = {http://pubs.acs.org/doi/abs/10.1021/jz1016894},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jz1016894}
}
@article{ludwiczek2013strategies,
  title={Strategies for Modulating the pH-Dependent Activity of a Family 11 Glycoside Hydrolase},
  author={Ludwiczek, Martin L and D’Angelo, Igor and Yalloway, Gary N and Brockerman, Jacob A and Okon, Mark and Nielsen, Jens E and Strynadka, Natalie CJ and Withers, Stephen G and McIntosh, Lawrence P},
  journal={Biochemistry},
  volume={52},
  number={18},
  pages={3138--3156},
  year={2013},
  publisher={ACS Publications}
}
@article{best03,
    author  =   "Bestbury, Bruce W.",
     title  =   "{$R$}-matrices and the magic square",
   journal  =   "J. Phys. A",
  fjournal  =   "Journal of Physics. A. Mathematical and General",
    volume  =   "36",
      year  =   "2003",
    number  =   "7",
     pages  =   "1947--1959",
      issn  =   "0305-4470",
     coden  =   "JPHAC5",
   mrclass  =   "17B10",
  mrnumber  =   "1 960 703"}

@article{hediger2013silico,
  title={In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB},
  author={Hediger, Martin R and De Vico, Luca and Rannes, Julie B and J{\"a}ckel, Christian and Besenmatter, Werner and Svendsen, Allan and Jensen, Jan H},
  journal={PeerJ},
  volume={1},
  pages={e145},
  year={2013},
  publisher={PeerJ Inc.}
}

@article{hediger2013computational,
  title={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},
  author={Hediger, Martin R and Steinmann, Casper and De Vico, Luca and Jensen, Jan H},
  journal={PeerJ},
  volume={1},
  pages={e111},
  year={2013},
  publisher={PeerJ Inc.}
}

@article{gotor2006candida,
  title={Candida antarctica lipase B: an ideal biocatalyst for the preparation of nitrogenated organic compounds},
  author={Gotor-Fern{\'a}ndez, Vicente and Busto, Eduardo and Gotor, Vicente},
  journal={Advanced synthesis \& catalysis},
  volume={348},
  number={7-8},
  pages={797--812},
  year={2006},
  publisher={Wiley Online Library}
}

@article{CBIC:CBIC200800318,
author = {Svedendahl, Maria and Carlqvist, Peter and Branneby, Cecilia and Allnér, Olof and Frise, Anton and Hult, Karl and Berglund, Per and Brinck, Tore},
title = {Direct Epoxidation in Candida antarctica Lipase B Studied by Experiment and Theory},
journal = {ChemBioChem},
volume = {9},
number = {15},
publisher = {WILEY-VCH Verlag},
issn = {1439-7633},
url = {http://dx.doi.org/10.1002/cbic.200800318},
doi = {10.1002/cbic.200800318},
pages = {2443--2451},
keywords = {catalytic promiscuity, enzyme catalysis, epoxidation, hydrolases, molecular dynamics},
year = {2008},
}
@article{rathore2013advances,
  title={Advances in Binding Free Energies Calculations: QM/MM-Based Free Energy Perturbation Method for Drug Design},
  author={Rathore, RS and Sumakanth, M and Reddy, M Siva and Reddanna, P and Rao, Allam Appa and Erion, Mark D and Reddy, MR},
  journal={Current pharmaceutical design},
  volume={19},
  number={26},
  pages={4674--4686},
  year={2013},
  publisher={Bentham Science Publishers}
}
@article{buch2011complete,
  title={Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations},
  author={Buch, Ignasi and Giorgino, Toni and De Fabritiis, Gianni},
  journal={Proceedings of the National Academy of Sciences},
  volume={108},
  number={25},
  pages={10184--10189},
  year={2011},
  publisher={National Acad Sciences}
}

@article{kirk2002industrial,
  title={Industrial enzyme applications},
  author={Kirk, Ole and Borchert, Torben Vedel and Fuglsang, Claus Crone},
  journal={Current opinion in biotechnology},
  volume={13},
  number={4},
  pages={345--351},
  year={2002},
  publisher={Elsevier}
}

@article{schmid2002use,
  title={The use of enzymes in the chemical industry in Europe},
  author={Schmid, Andreas and Hollmann, Frank and Park, Jin Byung and B{\"u}hler, Bruno},
  journal={Current Opinion in Biotechnology},
  volume={13},
  number={4},
  pages={359--366},
  year={2002},
  publisher={Elsevier}
}

@article{gao2006computational,
  title={Computational Design of a Human Butyrylcholinesterase Mutant for Accelerating Cocaine Hydrolysis Based on the Transition-State Simulation},
  author={Gao, Daquan and Cho, Hoon and Yang, Wenchao and Pan, Yongmei and Yang, Guangfu and Tai, Hsin-Hsiung and Zhan, Chang-Guo},
  journal={Angewandte Chemie International Edition},
  volume={45},
  number={4},
  pages={653--657},
  year={2006},
  publisher={Wiley Online Library}
}

@article{siegbahn2009recent,
  title={Recent developments of the quantum chemical cluster approach for modeling enzyme reactions},
  author={Siegbahn, Per EM and Himo, Fahmi},
  journal={JBIC Journal of Biological Inorganic Chemistry},
  volume={14},
  number={5},
  pages={643--651},
  year={2009},
  publisher={Springer}
}

@article{lonsdale2013quantum,
  title={Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9},
  author={Lonsdale, Richard and Houghton, Kerensa T and Zurek, Jolanta and Bathelt, Christine M and Foloppe, Nicolas and de Groot, Marcel J and Harvey, Jeremy N and Mulholland, Adrian J},
  journal={Journal of the American Chemical Society},
  volume={135},
  number={21},
  pages={8001--8015},
  year={2013},
  publisher={ACS Publications}
}

@article{liao2012comparison,
  title={Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase},
  author={Liao, Rong-Zhen and Thiel, Walter},
  journal={Journal of Chemical Theory and Computation},
  volume={8},
  number={10},
  pages={3793--3803},
  year={2012},
  publisher={ACS Publications}
}

@article{bajpai1999application,
  title={Application of enzymes in the pulp and paper industry},
  author={Bajpai, Pratima},
  journal={Biotechnology Progress},
  volume={15},
  number={2},
  pages={147--157},
  year={1999},
  publisher={Wiley Online Library}
}

@article{buchert1994application,
  title={Application of xylanases in the pulp and paper industry},
  author={Buchert, Johanna and Tenkanen, Maija and Kantelinen, Anne and Viikari, Liisa},
  journal={Bioresource technology},
  volume={50},
  number={1},
  pages={65--72},
  year={1994},
  publisher={Elsevier}
}

@article{uppenberg1994sequence,
  title={The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica},
  author={Uppenberg, Jonas and Hansen, Mogens Trier and Patkar, Shamkant and Jones, T Alwyn},
  journal={Structure},
  volume={2},
  number={4},
  pages={293--308},
  year={1994},
  publisher={Elsevier}
}

@article{chaput2012contribution,
  title={Contribution of both catalytic constant and Michaelis constant to CALB enantioselectivity: Use of FEP calculations for prediction studies},
  author={Chaput, L and Sanejouand, Y-H and Balloumi, Asma and Tran, Vinh and Graber, Marianne},
  journal={Journal of Molecular Catalysis B: Enzymatic},
  volume={76},
  pages={29--36},
  year={2012},
  publisher={Elsevier}
}

@article{agresti2010ultrahigh,
  title={Ultrahigh-throughput screening in drop-based microfluidics for directed evolution},
  author={Agresti, Jeremy J and Antipov, Eugene and Abate, Adam R and Ahn, Keunho and Rowat, Amy C and Baret, Jean-Christophe and Marquez, Manuel and Klibanov, Alexander M and Griffiths, Andrew D and Weitz, David A},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={9},
  pages={4004--4009},
  year={2010},
  publisher={National Acad Sciences}
}

@article{bornscheuer2004catalytic,
  title={Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways},
  author={Bornscheuer, Uwe T and Kazlauskas, Romas J},
  journal={Angewandte Chemie International Edition},
  volume={43},
  number={45},
  pages={6032--6040},
  year={2004},
  publisher={Wiley Online Library}
}

@article{gayot2003modification,
  title={Modification of flavonoid using lipase in non-conventional media: effect of the water content},
  author={Gayot, S and Santarelli, X and Coulon, D},
  journal={Journal of biotechnology},
  volume={101},
  number={1},
  pages={29--36},
  year={2003},
  publisher={Elsevier}
}

@article{ragauskas2006path,
  title={The path forward for biofuels and biomaterials},
  author={Ragauskas, Arthur J and Williams, Charlotte K and Davison, Brian H and Britovsek, George and Cairney, John and Eckert, Charles A and Frederick, William J and Hallett, Jason P and Leak, David J and Liotta, Charles L and others},
  journal={science},
  volume={311},
  number={5760},
  pages={484--489},
  year={2006},
  publisher={American Association for the Advancement of Science}
}

@article{zhang2011vital,
  title={What is vital (and not vital) to advance economically-competitive biofuels production},
  author={Zhang, Y-H Percival},
  journal={Process Biochemistry},
  volume={46},
  number={11},
  pages={2091--2110},
  year={2011},
  publisher={Elsevier}
}

@article{gao2013increased,
  title={Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis},
  author={Gao, Dahai and Chundawat, Shishir PS and Sethi, Anurag and Balan, Venkatesh and Gnanakaran, S and Dale, Bruce E},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={27},
  pages={10922--10927},
  year={2013},
  publisher={National Acad Sciences}
}

@article{yeoman2010thermostable,
  title={Thermostable enzymes as biocatalysts in the biofuel industry},
  author={Yeoman, Carl J and Han, Yejun and Dodd, Dylan and Schroeder, Charles M and Mackie, Roderick I and Cann, Isaac KO},
  journal={Advances in applied microbiology},
  volume={70},
  pages={1--55},
  year={2010},
  publisher={Elsevier}
}

@article{bowman2008qm,
  title={QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate},
  author={Bowman, Anna L and Grant, Ian M and Mulholland, Adrian J},
  journal={Chemical Communications},
  volume={37},
  pages={4425--4427},
  year={2008},
  publisher={Royal Society of Chemistry}
}

@book{cramer2013essentials,
  title={Essentials of computational chemistry: theories and models},
  author={Cramer, Christopher J},
  year={2013},
  publisher={John Wiley \& Sons}
}

@book{young2004computational,
  title={Computational chemistry: a practical guide for applying techniques to real world problems},
  author={Young, David},
  year={2004},
  publisher={John Wiley \& Sons}
}

@book{jensen2007introduction,
  title={Introduction to computational chemistry},
  author={Jensen, Frank},
  year={2007},
  publisher={John Wiley \& Sons}
}

@article{rezac2009semiempirical,
  title={Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes},
  author={Rez{\'a}c, Jan and Fanfrlik, Jindrich and Salahub, Dennis and Hobza, Pavel},
  journal={Journal of Chemical Theory and Computation},
  volume={5},
  number={7},
  pages={1749--1760},
  year={2009},
  publisher={ACS Publications}
}

@article{vrezavc2011halogen,
  title={A halogen-bonding correction for the semiempirical PM6 method},
  author={Rez{\'a}c, Jan and Hobza, Pavel},
  journal={Chemical Physics Letters},
  volume={506},
  number={4},
  pages={286--289},
  year={2011},
  publisher={Elsevier}
}

@article{bachega2013gtkdynamo,
  title={GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations},
  author={Bachega, Jos{\'e} Fernando R and Timmers, Lu{\'\i}s Fernando SM and Assirati, Lucas and Bachega, Leonardo R and Field, Martin J and Wymore, Troy},
  journal={Journal of computational chemistry},
  volume={34},
  number={25},
  pages={2190--2196},
  year={2013},
  publisher={Wiley Online Library}
}


@article{lind2013quantum,
  title={Quantum chemistry as a tool in asymmetric biocatalysis: Limonene epoxide hydrolase test case},
  author={Lind, Maria ES and Himo, Fahmi},
  journal={Angewandte Chemie},
  volume={125},
  number={17},
  pages={4661--4665},
  year={2013},
  publisher={Wiley Online Library}
}

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