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Knapp, Ernst Walter
Freie Universitaet Berlin
     
Degree   Prof. Dr.
Organisation   Freie Universitaet Berlin
Status   Group Leader
Telephone   +49 30 838 54387
Contact   knapp(at)chemie.fu-berlin.de
Homepage  
Born July 28, 1948
Academic Degrees
1973 University of Kaiserslautern, Germany
Diploma in Physics
1976 University of Kaiserslautern, Germany
Ph.D. in Physics
1985 Technical University Munich, Germany
Habilitation in Theoretical Physics
Employments
1974-1976 University of Kaiserslautern, Germany, Predoctoral Research Associate
1976-1977 Purdue University, Lafayette Ind. USA, NATO-Fellow
1978 Max-Planck-Institute of Biophysical Chemistry, Goettingen, Germany, Fellow
1979-1986 Technical University Munich, Research Associate
1986-1990 Heisenberg Fellow, Guest at Technical University Munich
since 1991 Professor for Macromolecular Modelling at FU Berlin, Chemistry Department
2001-2003 Director of the Institute of Chemistry
Memberships
Deutsche Physikalische Gesellschaft
Deutsche Gesellschaft fuer Biophysik

Publications

Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1
Photochemistry and Photobiology 93.3, 713-723., 2017
Takiden - Velazquez-Escobar - Dragelj - Woelke - Knapp - Piwowarski - Bartl - Hildebrandt - Mroginski

Empirical conversion of pKA values from water to other solvents: application to acetonitrile, dimethyl sulfoxide and methanol
, 2017
Rossini - Bochevarov - Knapp

Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations
BBA Bioenergetics 1858 103-108, 2017
Sezer - Woelke - Knapp - Schlesinger - Mroginski - Weidinger

Influence of heterogeneity on the ultrafast photoisomerization dynamics of Pfr in Cph1 phytochrome
Photochem. Photobiol. 93 703-712, 2017
Stensitzki - Yang - Wolke - Knapp - Hughes - Mroginski - Heyne

Proton solvation in protic and aprotic solvents
J. Comp. Chem. 37 1082-1091., 2016
Rossini - Knapp

CH/O interactions of aromatic CH donors within proteins: a crystallographic study
Cryst. Growth Des. 16, 1948-1957, 2016
Dragelj - Stankovic - Bozinovski - Meyer - Veljkovic - Medakovic - Knapp - Zaric

Chemically realistic tetrahedral lattice models for polymer chains: application to polyethylene oxide
J. Chem. Theory Comput. 12 2388-2400, 2016
Dietschreit - Diestler - Knapp

Computing pKA values in different solvents by electrostatic transform
J. Chem. Theory Comput. 12 3360-3369, 2016
Rossini - Netz - Knapp

Water dielectric effects in planar confinement
Phys. Rev. Lett. 117 048001, 2016
Schlaich - Knapp - Netz

Merging structural information from X-ray crystallography, quantum chemistry and EXAFS spectra: The oxygen evolving complex in PSII
J. Phys. Chem. B 120 10899- 10922, 2016
Chernev - Zaharieva - Rossini - Galstyan - Dau - Knapp

Protonation State-Dependent Communication in Cytochrome c Oxidase
Biophys. J. 111 492-503. , 2016
Helabad - Ghane - Reidelbach - Woelke - Knapp - Imhof

Computing pKa values of hexa-aqua transition metal complexes
J. Comp. Chem. 36 (2015) 69-78. , 2015
GGalstyan - Knapp

Mechanical rupture of mono- and bivalent transition metal complexes in experiment and theory
J. Phys. Chem. C 119 (2015) 4333-4343, 2015
Gensler - Eidamshaus - Galstyan - Knapp - Reissig - Rabe

pKA in proteins solving the PoissonBoltzmann equation with finite elements
J. Comput. Chem. 36 2147-2157, 2015
Sakalli - Knapp

ProPairs: A Data Set for Protein-Protein Docking
J Chem Inf Model, 2015, 55 (7), pp 1495-1507. , 2015
Krull - Korff - Elghobashi - Meinhardt - Knapp

Optimized distance-dependent atom-pair potential DOOP for protein structure prediction
Proteins-Struct Funct Bioinformatics 83 (2015) 881-890. , 2015
Chae - Krull - Knapp

Mechanical rupture of mono- and bivalent transition metal complexes in experiment and theory
J. Phys. Chem. C, 119, 4333-4343. , 2015
Gensler - Eidamshaus - Galstyan - Knapp - Reissig - Rabe

mFES: A robust molecular Finite Element Solver for electrostatic energy computations
J. Chem. Theory Comput. 10 5095-5112, 2014
Sakalli - Schoeberl - Knapp

Models for self-avoiding polymer chains on the tetrahedral lattice
Makromol. Theory Simulation 23 452-463, 2014
Dietschreit - Diestler - Knapp

PSII Manganese Cluster: Protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations
BBA Bioenergetics 1837 1316-1321. , 2014
Robertazzi - Galstyan - Knapp

Lysine 362 in Cytochrome c Oxidase Regulates Opening of the K-Channel via Changes in pKA and Conformation
BBA Bioenergetics 1837 1998-2003. , 2014
Woelke - GGalstyan - Knapp

Protein secondary structure classification revisited: Processing DSSP information with PSSC
J. Chem. Mod. Sim. 54 2166-2179, 2014
Zacharias - Knapp

Proton Transfer in the K-Channel Analogue of B-Type Cytochrome c Oxidase from Thermus thermophilus
Biophys. J. doi:10.1016/j.bpj.2014.09.010, 2014
Woelke - Wagner - GGalstyan - Meyer - Knapp

mFES: a Finite Element Solver of molecular solvation energies
Bioinformatics , 2014
Sakalli - Knapp

Optimized distance-dependent atom-pair potential DOOP for protein structure prediction
Proteins, 2014
Chae - Krull - Knapp

Database of protein complexes with multivalent binding ability: Bival#8208bind
Proteins: Structure, Function, and Bioinformatics 82 (5), 744-751, 2014
Meyer - Knapp

Geometry motivated alternative view on local protein backbone structures
Protein Science 22 1669 -1674, 2013
Zacharias - Knapp

Understanding Selectin Counter-Receptor Binding from Electrostatic Energy Computations and Experimental Binding Studies
J. Phys. Chem. B 117 16443-16454. , 2013
Woelke - Kuehne - Meyer - GGalstyan - Dernedde - Knapp

Exploring the Possible Role of Glu286 in CcO by Electrostatic Energy Computations Combined with Molecular Dynamics
J. Phys. Chem. B 117 12432-12441, 2013
Woelke - GGalstyan - Galstyan - Meyer - Heberle - Knapp

Influence of Spacer-Receptor Interactions on the Stability of Bivalent Ligand-Receptor Complexes
J. Phys. Chem. B, 116 (8), pp 2595 to 2604, 2012
Numata - Juneja - Diestler - Knapp

Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
J. Chem. Theory Comput., http://dx.doi.org/10.1021/ct200910z, 2012
Numata - Knapp

Protein secondary structure prediction with SPARROW
J. Chem. Inf. Mod. 52 545-556, 2012
Bettella - Rasinski - Knapp

Oxygen-evolving Mn cluster in photosystem II: protonation pattern and oxidation state in the crystal
JACS 134 7442-7449, 2012
Galstyan - Robertazzi - Knapp

Computations of 36 tautomer/isomer equilibria of different lactams
J. Phys. Chem. A 116 6885-6893, 2012
GGalstyan - Knapp

Multivalency as a Chemical Organization and Action Principle
Angew. Chem. Int. Ed. Engl. 51 10472-10498, 2012
Fasting - Schalley - Weber - Seitz - Hecht - Koksch - Dernedde - Graf - Knapp - Haag

Charge transport in the ClC-type chloride-proton anti-porter from Escherichia coli.
J Biol Chem., 28286(4):2976-86, 2011
Kieseritzky - Knapp

PolyAna: analyzing synonymous and nonsynonymous polymorphic sites.
Conserv Genet Resour., 13(3):429-431, 2011
Knapp - Irausquin - Friedman - Hughes

Electrostatic pK(a) computations in proteins: Role of internal cavities.
Proteins, 2011
Meyer - Kieseritzky - Knapp

Multivalent Binding of Formin-binding Protein 21 (FBP21)-Tandem-WW Domains Fosters Protein Recognition in the Pre-spliceosome.
J Biol Chem., 286(44):38478-87, 2011
Klippel - Wieczorek - Schuemann - Krause - Marg - Seidel - Meyer - Knapp - Freund

Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features.
BMC Bioinformatics., 12(1):412 , 2011
Demir-Kavuk - Kamada - Akutsu - Knapp

Recent advances in anion-pi interactions
Crystengcomm, 13(10): 3293-3300, 2011
Robertazzi - Krull - Knapp

Understanding properties of cofactors in proteins: redox potentials of synthetic cytochrome b
ChemPhysChem, 11, 1196-1206, 2010
Gamiz-Hernandez - Kieseritzky - Demir-Kavuk - Galstyan - Knapp

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
J. Chem. Theory Comput., 6 (6), pp 1871-1883, 2010
Juneja - Numata - Nilsson - Knapp

Exploring classification strategies with the CoEPrA 2006 contest.
Bioinformatics. 2010 Mar 126(5):603-9. Epub 2010 Jan 22., 2010
Demir-Kavuk - Riedesel - Knapp

Circular permuted proteins in the universe of protein folds.
Proteins. 1578(7):1618-30. , 2010
Schmidt-Goenner - Guerler - Kolbeck - Knapp

Strategies of non-sequential protein structure alignments.
Genome Inform. 22:21-9, 2010
Guerler - Knapp

Understanding properties of cofactors in proteins: redox potentials of synthetic cytochromes b.
Chemphyschem. 11(6):1196-206. , 2010
Gamiz-Hernandez - Kieseritzky - Galstyan - Demir-Kavuk - Knapp

GIS: a comprehensive source for protein structure similarities.
Nucleic Acids Res. 38:W46-52, 2010
Guerler - Knapp

Bound Ligand Conformer Revealed by Flexible Structure Alignment in Absence of Crystal Structures: Indirect Drug Design Probed for HIV-1 Protease Inhibitors
J. Chem. Theory Comput., 5 (3), pp 659-673 , 2009
Juneja - Riedesel - Hodoscek - Knapp

Symmetric structures in the universe of protein folds
J. Chem. Inf. Model., 2009, 49 (9), 2147-2151, 2009
Guerler - Wang - Knapp

Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes
J. Comput. Chem., v.30, p.203211, 2009
A.Galstyan, - E.W.Knapp

Circular permuted proteins in the universe of protein folds
Proteins, 78:7, p. 1618 - 1630, 2009
Schmidt-Goenner - Guerler - Knapp

Understanding rubredoxin redox potentials: role of H-bonds on model complexes
J. Chem. Theory Comput., 5, p.2898-2908, 2009
Gamiz-Hernandez - Galstyan - Knapp

Predicting protein complex geometries with a neural network
Proteins, 1026 - 1039, 2009
Chae - Krull - Lorenzen - Knapp

Superimpose - A 3D structural superposition server
Nucleic Acids Research 36, W47-W53, 2008
Bauer - Bourne - Formella - Froemmel - Gille - Goede - Guerler - Hoppe - Knapp - Pschel - Wittig - Ziegler - Preissner

Novel protein folds and their non-sequential structural analogs
Protein Science, 17:1374-82, 2008
Guerler - Knapp

Sampling geometries of protein-protein complexes
Genome Informatics Volume 20, 260-268, 2008
Guerler - Lorenzen - Krull - Knapp

Measuring correlations in metabolomic networks with mutual information
Genome Informatics Volume 20, 2008
Numata - Ebenhoeh - Knapp

Optimizing pKA computation in proteins with pH adapted conformations
Proteins 71 (3), 1335-1348, 2008
Kieseritzky - Knapp

Improved pKa prediction: Combining empirical and semimicroscopic methods
Journal of Computational Chemistry, 29 (15), 2575-2581, 2008
Kieseritzky - Knapp

Combined NMR and computational study for azide binding to human manganese superoxide dismutase
Solid State Nucl. Magn. Reson., 34, 6-13, 2008, 2008
Emmler - Ayala - Silverman - Hafner - A.Galstyan - Knapp - Buntkowsky

Protonation states of ammonia/ammonium in the hydrophobic pore of ammonia transporter protein AmtB
J. Am. Chem. Soc., in press, 2007
Ishikita - Knapp

Conformational entropy of biomolecules: Beyond the quasi-harmonic approximation
Genome Informatics Volume 18, 192-205, 2007
Numata - Wan - Knapp

Evaluation of sequence alignments of distantly related sequence pairs with respect to structural similarity
Genome Informatics Volume 18, 183-191, 2007
Guerler - Knapp

alpha-Helices direct excitation energy flow in the Fenna-Matthews-Olson protein
Proc Natl Acad Sci USA, 104, 16862, 2007
Mueh - Madjet - Adolphs - Abdurahman - Rabenstein - Ishikita - Knapp - Renger

Redox potential of the non-heme iron complex in bacterial photosynthetic reaction center
Biochim. Biophys. Acta, v.1767, p.1300-1309, 2007
H.Ishikita - A.Galstyan - E.W.Knapp

Cationic State of Accessory Chlorophyll and Electron Transfer through Pheophytin to Plastoquinone in Photosystem II
Angew. Chem. Int. Ed. Engl. 45 (2006) 1964-1965, 2006
Ishikita - Loll - Saenger - Knapp

How photosynthetic reaction centers control oxidation power in chlorophyll pairs P680, P700 and P870
Proc. Natl. Acad. Sci. USA 103 (2006) 9855-9860, 2006
Ishikita - Saenger - Biesiadka - Loll - Knapp

The role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study
J Biol Inorg Chem (2006) 11: 26?40, 2006
Morra - Knapp

Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study
J Biol Inorg Chem (2006) 11: 26-40, 2006
Kieseritzky - Morra - Knapp

Cationic state of accessory chlorophyll and electron transfer through pheophytin to plastoquinone in photosystem II
Angew. Chem. 118 (2006) 1998-1999, 2006
Ishikita - Biesiadka - Loll - Saenger - Knapp

Electrostatic influence of PsaC protein binding to the PsaA/PsaB heterodimer in Photosystem I
Biophys. J. 90 (2006) 1081-1089, 2006
Ishikita - Stehlik - Golbeck - Knapp

Energetics of a possible proton exit pathway for water oxidation in Photosystem II
Biochemistry 45 (2006) 2063-2071, 2006
Ishikita - Knapp - Saenger - Biesiadka - Loll

Function of redox active tyrosine in photosystem II
Biophys. J. 90 (2006) 3886-3896, 2006
Ishikita - Knapp

Electrostatic role of the non-heme iron complex in bacterial photosynthetic reaction center
FEBS Lett. (2006) in press, 2006
Ishikita - Knapp

Function of two b-carotenes near the D1 and D2 proteins in photosystem II dimers
Biochim. Biophys. Acta (Bioenergetics), in press, 2006
Ishikita - Loll - Biesiadka - Zouni - Saenger - Knapp

Connectivity independent protein fold detection: A hierarchical approach
BMC Bioinformatics 2006, 7:510, 2006
Kolbeck - May - Schmidt-Goenner - Steinke - Knapp

Redox potentials of chlorophylls in the photosystem II reaction center
Biochemistry (2005) 44, 4118-4124, 2005
Ishikita - Knapp - Saenger - Biesiadka - Loll

Energetics of proton transfer pathways in reaction centers from Rhodobacter sphaeroides: The Glu-H173 activated mutants
J. Biol. Chem. 280 (2005) 12446-12450, 2005
Ishikita - Knapp

Tuning electron transfer by ester-group of chlorophylls in bacterial photosynthetic reaction center
FEBS Lett. 579 (2005) 712-716, 2005
Ishikita - Loll - Biesiadka - Galstyan - Saenger - Knapp

Redox potentials of chlorophylls and beta-carotene in the antenna complexes of photosystem II
J. Am. Chem. Soc., 127 (6), 1963 -1968, 2005
Ishikita - Knapp

Control of quinone redox potentials in photosystem II: electron transfer and photoprotection
J. Am. Chem. Soc. (2005) 14714-14720, 2005
Ishikita - Knapp

Redox potential of cytochrome c550 in the cyanobacterium Thermosynechococcus elongatus
FEBS Lett. 579 (2005) 3190-3194, 2005
Ishikita - Knapp

Computational studies on energetics of imidazole heme conformations
J. Biol. Inorg. Chem., v.10, p.343-354, 2005
A.Galstyan - S.Zaric - E.W.Knapp

Oxidation of the non-heme iron complex in photosystem II
Biochemistry 44 (2005) 14772-14784, 2005
Knapp - Ishikita

Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers
Proc. Natl. Acad. Sci. USA 102 (2005) 16215-16220, 2005
Knapp - Ishikita

Variation of Ser-L223 hydrogen bonding with the QB redox state in reaction centers from Rhodobacter sphaeroides
J. Am. Chem. Soc. 126 (2004) 8059-8064, 2004
Knapp - Ishikita

Peptide binding at class I major histocompatibility complex scored with linear functions and support vector machines
Genome Informatics 15 (2004) 198-212, 2004
Riedesel - Kolbeck - Schmetzer - Knapp

A Kunitz type protease inhibitor related protein is synthesized in Drosophila prepupal salivary glands and released into the moulting fluid during pupation
Volume 34, Issue 8, Pages 731-877 (August 2004), 2004
Knapp - Schmidt-Busch - Saunders - Weise - Wedde - Vilcinskas

Accurate pKa Determination for a Heterogeneous Group of Organic Molecules
ChemPhysChem,Volume 5, Issue 10 , Pages 1513 - 1522, 2004
Knapp - Schmidt-Busch

A molecular docking study of estrogenically-active compounds with 1,2-diarylethane and 1,2-diarylethene pharmacophors
Bioorganic & Medicinal Chemistry 12 (2004) 6527?6537, 2004
Kekenes-Huskey - Knapp - Muegge - Rauch - Gust

Redox Potential of Quinones in Photosynthetic Reaction Centers from Rhodobacter sphaeroides: Dependence on Protonation of Glu-L212 and Asp-L213
Biochemistry 2003, 42, 3882-3892, 2003
Ishikita - Morra - Knapp

Tuning Heme Redox Potentials in the Cytochrome c Subunit of Photosynthetic Reaction Centers
J. Biol. Chem., Dec 2003; 278: 51993 - 52001, 2003
Voigt - Knapp

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I
J. Biol. Chem. 278 (2003) 52002-52011, 2003
Knapp - Ishikita

Unfolding of the cold shock protein studied with biased molecular dynamics
Proteins 53 (2003) 597?606, 2003
Morra - Knapp - Hodoscek

Energetics of Radical Transfer in DNA Photolyase
J. AM. CHEM. SOC. 2002, 124, 3775-3782, 2002
Zmiric - Popovic - Knapp - Zaric

Driving forces of protein association: The dimer-octamer equilibrium in arylsulfatase A
17.Biophys. J. 83 (2002) 3066-3078., 2002
Knapp - Saenger - Vagedes

Protonation and Stability of the Globular Domain of Influenza Virus Hemagglutinin
Biophys. J. 82 (2002) 1050-1058, 2002
Knapp - Huang - Opitz

How to guarantee optimal stability for most representative structures in the protein data bank
Proteins 44 (2001) 79-96, 2001
Bastolla - Farwer - Knapp - Vendruscolo

Artificial Cytochrome b: Computer Modeling and Evaluation of Redox Potentials
J. Am. Chem. Soc. 123 (2001) 6040-6053, 2001
Popovic - Zaric - Rabenstein - Knapp

Factors Determining the Orientation of Axially Coordinated Imidazoles in Heme Proteins
Biochemistry 40 (2001) 7914-7928, 2001
Zaric - Popovic - Knapp

Calculated pH-Dependent Population and Protonation of Carbon-Monoxy-Myoglobin Conformers
Biophys. J. 80 (2001) 1141-1150, 2001
Rabenstein - Knapp

The X-ray absorption spectroscopy Debye-Waller factors of an iron compound and of met-myoglobin as a function of temperature
Europ. Biophys. J. 30 (2001) 393-403, 2001
Knapp - et - al.

The Deacylation Step of Acetylcholinesterase: Computer Simulation Studies
J. Am. Chem. Soc. 2000, 122, 12254-12262, 2000
Knapp - Vagedes - Marelius - Aaqvist - Rabenstein

Electron Transfer between the Quinones in the Photosynthetic Reaction Center and Its Coupling to Con
Biochemistry 2000, 39, 10487-10496, 2000
Rabenstein - Ullmann - Knapp

Structural Alignment of Ferredoxin and Flavodoxin Based on Electrostatic Potentials: Implications fo
Proteins 38 (2000) 301-309, 2000
Ullmann - Knapp - Hauswald

Metal ligand-aromatic cation-( interactions in metallo-proteins: ligands coordinated to metal intera
Chem. Eur. J. 6 (2000) 3935-3942, 2000
Zaric - Popovic - Knapp

Diffusion of water molecules in crystalline small beta, Greek-cyclodextrin hydrates
Journal of Molecular Graphics and Modelling 18 (2000) 143-152, 167-168., 2000
Braesicke - Saenger - Knapp - Steiner

Electrostatic models for computing protonation and redox equilibria in proteins
Eur. Biophys. J. 28 (1999) 533-551 (invited review), 1999
Ullmann - Knapp

Energetics of Electron-Transfer and Protonation Reactions of the Quinones in the Photosynthetic Reaction Center of Rhodopseudomonas Viridis
Biochemistry 37 (1998) 2488-2495, 1998
Rabenstein - Ullmann - Knapp

An energy function for dynamics simulations of polypeptides in torsion angle space
J. Chem. Phys. (1998) 108, 8264-8276, 1998
Knapp

Protonation patterns for the different states of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis
Eur. Biophys. J. 27 (1998) 626-637, 1998
Rabenstein - Ullmann - Knapp

Computational Simulation and Analysis of Dynamic Association between Plastocyanin and Cytochrome f. Consequences for the Electron-Transfer Reaction
J. Am. Chem. Soc., 119, 42-52, 1997
Ullmann - Knapp - Kostic

Folding pathways of a helix-turn-helix model protein
J. Phys. Chem. B101 (1997) 6734-6740, 1997
Knapp - Hoffmann

Comparison of the physiologically-equivalent proteins cytochrome c6 and plastocyanin on the basis their electrostatic potentials. Tryptophane 63 in cytochrome c6 may be isofunctional with tyrosine 83 in plastocyanin
Biochemistry 36 (1997) 16187-16196, 1997
Ullmann - Hauswald - Kostic - Knapp

The influence of the Pauli exclusion principle on electron impact ionization of light atoms
J. Phys. B: Atom. Molec. Phys. 6 (1973) 2516-2528, 1973
Knapp

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+49 30 838 54387
+49 30 838 56921 (Fax)


Protein Electrostatics 2016

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Selected publications

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Aysam Guerler, Connie Wang and E. W. Knapp


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Alok Juneja, Henning Riedesel, Milan Hodoscek and E. W. Knapp


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Gegham Galstyan and E. W. Knapp


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Ilkay Sakalli and E. W. Knapp


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