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
pKa Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories
J. Chem. Theory Comput. 11, 2827-2840, 2015
Meyer - Knapp
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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