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List of works by Henry van den Bedem

A Structural Basis for the Regulatory Inactivation of DnaA

scientific article

A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution

scientific article

A geometric approach to characterize rigidity in proteins

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

scientific article

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

article

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

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

Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces

scientific article published on 5 January 2018

Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution

scientific article published in November 2006

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

scientific article published on 26 February 2020

Computing Protein Structures from Electron Density Maps: The Missing Fragment Problem

Conformational changes associated with the binding of zinc acetate at the putative active site of Xc TcmJ, a cupin from Xanthomonas campestris pv. campestris

scientific article

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

scientific article published on January 2017

Cryo-EM structures of vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution

scientific article published on 20 March 2019

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

scientific article

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

scientific article

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

scientific article

Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution

scientific article

Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site

scientific article

Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution

scientific article

Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

article

Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate

scientific article

Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases

scientific 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 S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold

scientific article

Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function

scientific article published in July 2007

Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

scientific article published in June 2006

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

scientific article

Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold

article

Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

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 glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution

scientific article published in July 2004

Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution

scientific article

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

scientific article

Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution

scientific article published in August 2004

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

scientific article

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

scientific article

Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution

scientific article published in May 2004

Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

scientific article

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 a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution

scientific article published in March 2004

Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold

scientific article

Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution

scientific journal article

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

scientific article

Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

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 a transcription regulator (TM1602) from Thermotoga maritima at 2.3 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

Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution

scientific article

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

scientific article

Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution

scientific article

Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution

scientific article

Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution

scientific article published in March 2004

Crystal structure of an ORFan protein (TM1622) fromThermotoga maritimaat 1.75 Å resolution reveals a fold similar to the Ran-binding protein Mog1p

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 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 an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

scientific article

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

scientific article

Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

scientific article published in May 2004

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

scientific article

Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold

scientific article published in August 2004

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

scientific article

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution

scientific article

Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution

scientific article published in October 2006

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution

scientific article

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

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

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 structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

scientific article

Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold

scientific article

Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold

scientific article

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

scientific article

Discovering and Manipulating Protein Conformational Heterogeneity and Function

Distributed structure determination at the JCSG.

scientific article

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

Efficient algorithms to explore conformation spaces of flexible protein loops

scientific article published on October 2008

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

scientific article

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

Frustration-guided motion planning reveals conformational transitions in proteins

scientific article published on 9 June 2017

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

scientific article published in October 2015

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

scientific article

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

scientific article

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

scientific article

KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids

Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion

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

scientific article published on 30 September 2015

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

scientific article published on 04 December 2019

Modeling Structural Heterogeneity in Proteins from X-Ray Data

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

scientific article

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs

scientific article (publication date: July 2015)

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

scientific article published on 13 June 2018

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

scientific article

Radiation damage effects on protein conformation at room temperature and 100K

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

scientific article

Reply to 'Misreading chaperone-substrate complexes from random noise'

scholarly article by Scott Horowitz published in October 2018

Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation

scientific article published on 13 June 2019

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

scientific article

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

scientific article

Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules

scientific article

Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism

scientific article

Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism

scientific article

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

scientific article

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15

scientific article

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

scientific article

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

scientific article

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation

scientific article

Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

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

Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism

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

Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

scientific article

The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

scientific article

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

scientific article

The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes

scientific article

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

scientific article

The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae , reveals an OB-fold

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

The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

scientific article

The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

scientific article

Transport Properties of Nanoporous, Chemically Forced Biological Lattices

scientific article published on 27 November 2019

Visualizing chaperone-assisted protein folding.

scientific article published on 30 May 2016

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

scientific article published on 18 November 2020

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps

scientific article published on 06 December 2018

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

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