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Herman Berendsen

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Concepts & Ideas

Activities & Behaviors

Computer Simulation

Occupations

Chemicals & Drugs

Phenomena

Genes & Molecular Sequences

Amino Acid Sequence

Physiology

Protein Folding

Anatomy

Lipid Bilayers

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Co-Publications
Name
14
Amadei, Andrea
11
de Groot, BL
10
Tieleman, Peter
10
van Aalten, Daan
9
van Gunsteren, Wilfred
6
Kamman, Richard
5
Sansom, MS
5
Scheek, Ruud
5
Mark, Alan
5
Hayward, Steven
4
Findlay, John
4
Groenhof, Gerrit
3
Hess, Berk
3
Di Nola, Alfredo
3
Sansom, Mark

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Publications

TOP 3
Van Der Spoel David; Lindahl Erik; Hess Berk; Groenhof Gerrit; Mark Alan E; Berendsen Herman J C
GROMACS: fast, flexible, and free.
van den Bosch Marieke; Swart Marcel; Snijders Jaap G; Berendsen Herman J C; Mark Alan E; Oostenbrink Chris; van Gunsteren Wilfred F; Canters Gerard W
Calculation of the redox potential of the protein azurin and some mutants.
Saint-Martin Humberto; Hess Berk; Berendsen Herman J C
An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model.

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All Publications

2005: Van Der Spoel David; Lindahl Erik; Hess Berk; Groenhof Gerrit; Mark Alan E; Berendsen Herman J C
GROMACS: fast, flexible, and free.
Journal of computational chemistry 2005;26(16):1701-18.
2005: van den Bosch Marieke; Swart Marcel; Snijders Jaap G; Berendsen Herman J C; Mark Alan E; Oostenbrink Chris; van Gunsteren Wilfred F; Canters Gerard W
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem : a European journal of chemical biology 2005;6(4):738-46.
2004: Saint-Martin Humberto; Hess Berk; Berendsen Herman J C
An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model.
The Journal of chemical physics 2004;120(23):11133-43.
2004: Groenhof Gerrit; Bouxin-Cademartory Mathieu; Hess Berk; De Visser Sam P; Berendsen Herman J C; Olivucci Massimo; Mark Alan E; Robb Michael A
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
Journal of the American Chemical Society 2004;126(13):4228-33.
2003: Berendsen Herman J C
Inter-union bioinformatics group report.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 4):777-82.
2002: Garnier Jean; Berendsen Herman J C
International unions concerned about biodata.
Nature 2002;419(6909):777.
2002: Flohil J A; Vriend G; Berendsen H J C
Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.
Proteins 2002;48(4):593-604.
2002: Groenhof Gerrit; Lensink Marc F; Berendsen Herman J C; Mark Alan E
Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes.
Proteins 2002;48(2):212-9.
2002: Groenhof Gerrit; Lensink Marc F; Berendsen Herman J C; Snijders Jaap G; Mark Alan E
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore.
Proteins 2002;48(2):202-11.
2002: van Lune Franciska; Manning Linda; Dijkstra Klaas; Berendsen Herman J C; Scheek Ruud M
Order-parameter tensor description of HPr in a medium of oriented bicelles.
Journal of biomolecular NMR 2002;23(3):169-79.
2002: Pikkemaat Mariël G; Linssen Antonius B M; Berendsen Herman J C; Janssen Dick B
Molecular dynamics simulations as a tool for improving protein stability.
Protein engineering 2002;15(3):185-92.
2001: Creveld L D; Meijberg W; Berendsen H J; Pepermans H A
DSC studies of Fusarium solani pisi cutinase: consequences for stability in the presence of surfactants.
Biophysical chemistry 2001;92(1-2):65-75.
2001: Tieleman D P; Berendsen H J; Sansom M S
Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces.
Biophysical journal 2001;80(1):331-46.
2000: Berendsen H J; Hayward S
Collective protein dynamics in relation to function.
Current opinion in structural biology 2000;10(2):165-9.
1999: Kouwijzer M L; Berendsen H J; Grootenhuis P D
Computer simulations of the dynamics of human choriogonadotropin and its alpha subunit.
Proteins 1999;37(4):668-82.
1999: Roccatano D; Amadei A; Di Nola A; Berendsen H J
A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G.
Protein science : a publication of the Protein Society 1999;8(10):2130-43.
1999: Tieleman D P; Berendsen H J; Sansom M S
Surface binding of alamethicin stabilizes its helical structure: molecular dynamics simulations.
Biophysical journal 1999;76(6):3186-91.
1999: Amadei A; de Groot B L; Ceruso M A; Paci M; Di Nola A; Berendsen H J
A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells.
Proteins 1999;35(3):283-92.
1999: Tieleman D P; Berendsen H J; Sansom M S
An alamethicin channel in a lipid bilayer: molecular dynamics simulations.
Biophysical journal 1999;76(4):1757-69.
1999: de Groot B L; Vriend G; Berendsen H J
Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism.
Journal of molecular biology 1999;286(4):1241-9.
1999: Tieleman D P; Sansom M S; Berendsen H J
Alamethicin helices in a bilayer and in solution: molecular dynamics simulations.
Biophysical journal 1999;76(1 Pt 1):40-9.
1999: Sansom M S; Tieleman D P; Berendsen H J
The mechanism of channel formation by alamethicin as viewed by molecular dynamics simulations.
Novartis Foundation symposium 1999;225():128-41; discussion 141-5.
1998: Tieleman D P; Forrest L R; Sansom M S; Berendsen H J
Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations.
Biochemistry 1998;37(50):17554-61.
1998: Creveld L D; Amadei A; van Schaik R C; Pepermans H A; de Vlieg J; Berendsen H J
Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations.
Proteins 1998;33(2):253-64.
1998: Berendsen H J
A glimpse of the Holy Grail?
Science (New York, N.Y.) 1998;282(5389):642-3.
1998: Sansom M S; Tieleman D P; Forrest L R; Berendsen H J
Molecular dynamics simulations of membranes with embedded proteins and peptides: porin, alamethicin and influenza virus M2.
Biochemical Society transactions 1998;26(3):438-43.
1998: Tieleman D P; Berendsen H J
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.
Biophysical journal 1998;74(6):2786-801.
1998: de Groot B L; Hayward S; van Aalten D M; Amadei A; Berendsen H J
Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.
Proteins 1998;31(2):116-27.
1998: Hayward S; Berendsen H J
Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.
Proteins 1998;30(2):144-54.
1998: Tieleman D P; Breed J; Berendsen H J; Sansom M S
Alamethicin channels in a membrane: molecular dynamics simulations.
Faraday discussions 1998;(111):209-23; discussion 225-46.
1997: van Aalten D M; Conn D A; de Groot B L; Berendsen H J; Findlay J B; Amadei A
Protein dynamics derived from clusters of crystal structures.
Biophysical journal 1997;73(6):2891-6.
1997: de Groot B L; van Aalten D M; Scheek R M; Amadei A; Vriend G; Berendsen H J
Prediction of protein conformational freedom from distance constraints.
Proteins 1997;29(2):240-51.
1997: van der Spoel D; Berendsen H J
Molecular dynamics simulations of Leu-enkephalin in water and DMSO.
Biophysical journal 1997;72(5):2032-41.
1997: Hayward S; Kitao A; Berendsen H J
Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme.
Proteins 1997;27(3):425-37.
1996: van der Spoel D; Feenstra K A; Hemminga M A; Berendsen H J
Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions.
Biophysical journal 1996;71(6):2920-32.
1996: de Groot B L; Amadei A; Scheek R M; van Nuland N A; Berendsen H J
An extended sampling of the configurational space of HPr from E. coli.
Proteins 1996;26(3):314-22.
1996: van der Spoel D; van Buuren A R; Tieleman D P; Berendsen H J
Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions.
Journal of biomolecular NMR 1996;8(3):229-38.
1996: Lijnzaad P; Berendsen H J; Argos P
A method for detecting hydrophobic patches on protein surfaces.
Proteins 1996;26(2):192-203.
1996: van Aalten D M; de Groot B L; Berendsen H J; Findlay J B
Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins.
The Biochemical journal 1996;319 ( Pt 2)():543-50.
1996: van der Spoel D; de Groot B L; Hayward S; Berendsen H J; Vogel H J
Bending of the calmodulin central helix: a theoretical study.
Protein science : a publication of the Protein Society 1996;5(10):2044-53.
1996: de Groot B L; van Aalten D M; Amadei A; Berendsen H J
The consistency of large concerted motions in proteins in molecular dynamics simulations.
Biophysical journal 1996;71(4):1707-13.
1996: Marrink S J; Jähnig F; Berendsen H J
Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations.
Biophysical journal 1996;71(2):632-47.
1996: Lijnzaad P; Berendsen H J; Argos P
Hydrophobic patches on the surfaces of protein structures.
Proteins 1996;25(3):389-97.
1996: van der Spoel D; Vogel H J; Berendsen H J
Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein.
Proteins 1996;24(4):450-66.
1996: de Groot B L; Amadei A; van Aalten D M; Berendsen H J
Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.
Journal of biomolecular structure & dynamics 1996;13(5):741-51.
1996: Amadei A; Linssen A B; de Groot B L; van Aalten D M; Berendsen H J
An efficient method for sampling the essential subspace of proteins.
Journal of biomolecular structure & dynamics 1996;13(4):615-25.
1996: van Aalten D M; Amadei A; Bywater R; Findlay J B; Berendsen H J; Sander C; Stouten P F
A comparison of structural and dynamic properties of different simulation methods applied to SH3.
Biophysical journal 1996;70(2):684-92.
1996: Berendsen H J
Bio-molecular dynamics comes of age.
Science (New York, N.Y.) 1996;271(5251):954-5.
1996: van der Spoel D; Berendsen H J
Determination of proton transfer rate constants using Ab initio, molecular dynamics and density matrix evolution calculations.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():624-37.
1995: van Aalten D M; Findlay J B; Amadei A; Berendsen H J
Essential dynamics of the cellular retinol-binding protein--evidence for ligand-induced conformational changes.
Protein engineering 1995;8(11):1129-35.
1995: van Aalten D M; Amadei A; Linssen A B; Eijsink V G; Vriend G; Berendsen H J
The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water.
Proteins 1995;22(1):45-54.
1994: Tissen J T; Drenth J; Berendsen H J; Fraaije J G
Microhydrodynamics simulation of protein crystallization. I. Static calculations.
Biophysical journal 1994;67(5):1801-5.
1994: Tissen J T; Fraaije J G; Drenth J; Berendsen H J
Mesoscopic theories for protein crystal growth.
Acta crystallographica. Section D, Biological crystallography 1994;50(Pt 4):569-71.
1994: Di Nola A; Roccatano D; Berendsen H J
Molecular dynamics simulation of the docking of substrates to proteins.
Proteins 1994;19(3):174-82.
1994: van Nuland N A; Hangyi I W; van Schaik R C; Berendsen H J; van Gunsteren W F; Scheek R M; Robillard G T
The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data.
Journal of molecular biology 1994;237(5):544-59.
1994: Leenders R; van Gunsteren W F; Berendsen H J; Visser A J
Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin.
Biophysical journal 1994;66(3 Pt 1):634-45.
1994: Egberts E; Marrink S J; Berendsen H J
Molecular dynamics simulation of a phospholipid membrane.
European biophysics journal : EBJ 1994;22(6):423-36.
1993: van Schaik R C; Berendsen H J; Torda A E; van Gunsteren W F
A structure refinement method based on molecular dynamics in four spatial dimensions.
Journal of molecular biology 1993;234(3):751-62.
1993: Amadei A; Linssen A B; Berendsen H J
Essential dynamics of proteins.
Proteins 1993;17(4):412-25.
1993: Van Buuren A R; Berendsen H J
Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol.
Biopolymers 1993;33(8):1159-66.
1993: Heiner A P; Berendsen H J; van Gunsteren W F
Structure prediction of subtilisin BPN' mutants using molecular dynamics methods.
Protein engineering 1993;6(4):397-408.
1992: Heiner A P; Berendsen H J; van Gunsteren W F
MD simulation of subtilisin BPN' in a crystal environment.
Proteins 1992;14(4):451-64.
1992: van Schaik R C; van Gunsteren W F; Berendsen H J
Conformational search by potential energy annealing: algorithm and application to cyclosporin A.
Journal of computer-aided molecular design 1992;6(2):97-112.
1990: van Mierlo C P; Lijnzaad P; Vervoort J; Müller F; Berendsen H J; de Vlieg J
Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional 1H-NMR and restrained molecular dynamics.
European journal of biochemistry / FEBS 1990;194(1):185-98.
1990: Kamman R L; Go K G; Berendsen H J
Proton-nuclear magnetic resonance relaxation times in brain edema.
Advances in neurology 1990;52():401-5.
1989: Makinen M W; Troyer J M; van der Werff H; Berendsen H J; van Gunsteren W F
Dynamical structure of carboxypeptidase A.
Journal of molecular biology 1989;207(1):201-16.
1989: Kamman R L; Stomp G P; Berendsen H J
Unified multiple-feature color display for MR images.
Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine 1989;9(2):240-53.
1989: de Vlieg J; Berendsen H J; van Gunsteren W F
An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution.
Proteins 1989;6(2):104-27.
1988: Berendsen H J
Dynamic simulation as an essential tool in molecular modeling.
Journal of computer-aided molecular design 1988;2(3):217-21.
1988: Kamman R L; Go K G; Brouwer W; Berendsen H J
Nuclear magnetic resonance relaxation in experimental brain edema: effects of water concentration, protein concentration, and temperature.
Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine 1988;6(3):265-74.
1988: de Vlieg J; Scheek R M; van Gunsteren W F; Berendsen H J; Kaptein R; Thomason J
Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli.
Proteins 1988;3(4):209-18.
1987: van Gunsteren W F; Berendsen H J
Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.
Journal of computer-aided molecular design 1987;1(2):171-6.
1987: Kamman R L; Bakker C J; van Dijk P; Stomp G P; Heiner A P; Berendsen H J
Multi-exponential relaxation analysis with MR imaging and NMR spectroscopy using fat-water systems.
Magnetic resonance imaging 1987;5(5):381-92.
1985: Kamman R L; Go K G; Stomp G P; Hulstaert C E; Berendsen H J
Changes of relaxation times T1 and T2 in rat tissues after biopsy and fixation.
Magnetic resonance imaging 1985;3(3):245-50.
1984: Kamman R L; Go K G; Muskiet F A; Stomp G P; Van Dijk P; Berendsen H J
Proton spin relaxation studies of fatty tissue and cerebral white matter.
Magnetic resonance imaging 1984;2(3):211-20.

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