List of works - Henry van den Bedem

Accessing protein conformational ensembles using room-temperature X-ray crystallography

scientific article

Integrative, dynamic structural biology at atomic resolution—it's about time

scientific article published on April 1, 2015

Automated identification of functional dynamic contact networks from X-ray crystallography

scientific article

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

scientific article

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

scientific article

Automated diffraction image analysis and spot searching for high-throughput crystal screening

article

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

scientific article

Structure of the γ- D -glutamyl- L -diamino acid endopeptidase YkfC from Bacillus cereus in complex with L -Ala-γ- D -Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

scientific article

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

scientific article published on 30 September 2015

Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase

scientific article

Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold

scientific article published in November 2005

Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution

scientific article

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

scientific article

Real-space protein-model completion: an inverse-kinematics approach

scientific article

Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

scientific article

Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA

scientific article

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

scientific article

Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

scientific article

Efficient algorithms to explore conformation spaces of flexible protein loops

scientific article published on October 2008

Visualizing chaperone-assisted protein folding.

scientific article published on 30 May 2016

Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

scientific article

Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

scientific article

Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

scientific article

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution

scientific article

Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron

scientific article

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

scientific article

Characterizing RNA ensembles from NMR data with kinematic models

scientific article

Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution

scientific article

Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

scientific article published in June 2004

Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution

scientific article

Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes

scientific article

Distributed structure determination at the JCSG.

scientific article

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

scientific article

Conformational variation of proteins at room temperature is not dominated by radiation damage.

scientific article published on January 2017

Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution

scientific article published in July 2004

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

scientific article published in March 2004

Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution

scientific article

Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution.

scientific article published in May 2004

A Structural Basis for the Regulatory Inactivation of DnaA

scientific article

Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus

scientific article

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

scientific article published on 13 June 2018

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold

article

Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution

scientific article published in August 2004

Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

scientific article published in March 2005

Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

scientific article

Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

scientific article

Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold

article

Crystal structure of a novel archaeal AAA+ ATPase SSO1545 fromSulfolobus solfataricus

scientific article

Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

scientific article

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

scientific article

List of works by Henry van den Bedem

Accessing protein conformational ensembles using room-temperature X-ray crystallography

Integrative, dynamic structural biology at atomic resolution—it's about time

Automated identification of functional dynamic contact networks from X-ray crystallography

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

Automated diffraction image analysis and spot searching for high-throughput crystal screening

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

Structure of the γ- D -glutamyl- L -diamino acid endopeptidase YkfC from Bacillus cereus in complex with L -Ala-γ- D -Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase

Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold

Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

Real-space protein-model completion: an inverse-kinematics approach

Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

Efficient algorithms to explore conformation spaces of flexible protein loops

Visualizing chaperone-assisted protein folding.

Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution

Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Characterizing RNA ensembles from NMR data with kinematic models

Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution

Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution

Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes

Distributed structure determination at the JCSG.

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

Conformational variation of proteins at room temperature is not dominated by radiation damage.

Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution

Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution.

A Structural Basis for the Regulatory Inactivation of DnaA

Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold

Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution

Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold

Crystal structure of a novel archaeal AAA+ ATPase SSO1545 fromSulfolobus solfataricus

Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction