D. Hall

发表

Structural conservation of druggable hot spots in protein–protein interfaces

Laurie E. Grove, S. Vajda, D. Kozakov, 2011, Proceedings of the National Academy of Sciences.

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking.

Dima Kozakov, Sandor Vajda, Dzmitry Padhorny, 2017, Journal of molecular biology.

Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication

S. Vajda, R. Dingledine, D. Kozakov, 2011, Journal of Virology.

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.

Kathryn A. Porter, S. Vajda, J. Wells, 2019, Journal of medicinal chemistry.

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19)

D. Stuart, D. Hall, F. von Delft, 2020 .

The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.

G A Leonard, W N Hunter, D. Hall, 1999, Journal of molecular biology.

Encounter complexes and dimensionality reduction in protein–protein association

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, eLife.

Computational solvent mapping in structure-based drug design.

D. Hall, I. Enyedy, 2015, Future medicinal chemistry.

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Trends in pharmacological sciences.

New Frontiers in Druggability.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Journal of medicinal chemistry.

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues*

D. Hall, M. Hammel, R. Nikolaienko, 2016, The Journal of Biological Chemistry.

Analysis of protein binding sites by computational solvent mapping.

Dima Kozakov, Sandor Vajda, David R Hall, 2012, Methods in molecular biology.

Exploring the structural origins of cryptic sites on proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2018, Proceedings of the National Academy of Sciences.

The crystal and molecular structures of diferric porcine and rabbit serum transferrins at resolutions of 2.15 and 2.60 A, respectively.

D. Hall, G. Leonard, M. Winn, 2002, Acta crystallographica. Section D, Biological crystallography.

Aspirin inhibition of prostaglandin synthesis impairs egg development across mosquito taxa

D. Hall, Shabbir Ahmed, Yonggyun Kim, 2020, bioRxiv.

Communication between subunits within an archaeal clamp‐loader complex

D. Hall, N. Cook, D. Wigley, 2006, The EMBO journal.

Structure of Tagatose-1,6-bisphosphate Aldolase

D. Hall, W. Hunter, C. Bond, 2002, The Journal of Biological Chemistry.

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

D. Hall, M. Walsh, S. Culurgioni, 2017, Journal of visualized experiments : JoVE.

URIDINE MONOPHOSPHATE KINASE: A NEW GENETIC MARKER OF SUSCEPTIBILITY TO HAEMOPHILUS INFLUENZAE TYPE B DISEASE: 158

J. Rotter, D. Hall, G. Petersen, 1985, Pediatric Research.

D. Hall, I. Gutsche, L. Terradot, 2007, Molecular microbiology.

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Nucleic acids research.

89 Computational mapping reveals effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

Brandon S. Zerbe, S. Vajda, D. Kozakov, 2013 .

Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli.

D. Hall, W. Hunter, G. Leonard, 1999, Acta crystallographica. Section D, Biological crystallography.

The Antigenic Anatomy of SARS-CoV-2 Receptor Binding Domain

D. Stuart, P. Klenerman, J. Knight, 2020, SSRN Electronic Journal.

Stimulators of translation identified during a small molecule screening campaign.

S. Vajda, D. Kozakov, D. Hall, 2014, Analytical biochemistry.

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).

D. Stuart, D. Hall, F. von Delft, 2020 .

A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75

P. Klenerman, D. Hall, G. Screaton, 2022, Cell Reports.

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs.

S. Vajda, D. Hall, D. Beglov, 2016, Drug discovery today.

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, Bioinform..

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-associated Protein 1 (KEAP1) and Nuclear Factor, Erythroid 2 Like 2 (Nrf2).

Karen N. Allen, Amanda E. Wakefield, S. Vajda, 2019, Biochemistry.

BIOINFORMATICS APPLICATIONS NOTE

Dima Kozakov, Sandor Vajda, David R. Hall, 2022 .

The ClusPro web server for protein–protein docking

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Nature Protocols.

How good is automated protein docking?

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Proteins.

Identification of a prostaglandin E2 receptor that regulates mosquito oenocytoid immune cell function in limiting bacteria and parasite infection

D. Hall, Ryan C. Smith, Hyeogsun Kwon, 2020, bioRxiv.

Uridine monophosphate kinase and susceptibility to invasive Haemophilus influenzae type B disease.

J. Rotter, D. Hall, G. Petersen, 1986, Advances in experimental medicine and biology.

Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F

S. Vajda, R. Dingledine, D. Kozakov, 2010, Proceedings of the National Academy of Sciences.

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2015, Nature Protocols.

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

D. Stuart, P. Klenerman, J. Knight, 2021, Cell.

Structure of Class II Tagatose-1 , 6-bisphosphate Aldolase 22019

D. Hall, W. Hunter, C. Bond, 2016 .

New additions to the ClusPro server motivated by CAPRI

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Proteins.

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

The antigenic anatomy of SARS-CoV-2 receptor binding domain

D. Stuart, P. Klenerman, J. Knight, 2021, Cell.

Application of asymmetric statistical potentials to antibody-protein docking

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Bioinform..

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.

D. Hall, S. McSweeney, M. Ökvist, 2015, Journal of structural biology.

The high‐resolution crystal structure of the molybdate‐dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds

D. Hall, W. Hunter, G. Leonard, 1999, The EMBO journal.

Antibody evasion by the P.1 strain of SARS-CoV-2

D. Stuart, P. Klenerman, J. Knight, 2021, Cell.

Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

D. Stuart, P. Klenerman, J. Knight, 2021, bioRxiv.

RadA protein from Archaeoglobus fulgidus forms rings, nucleoprotein filaments and catalyses homologous recombination.

S. West, D. Hall, D. Wigley, 2001, Nucleic acids research.

Crystal structure and DNA‐binding analysis of RecO from Deinococcus radiodurans

D. Hall, S. McSweeney, I. Leiros, 2005, The EMBO journal.

Protein–ligand docking using FFT based sampling: D3R case study

Mohammad Moghadasi, Dima Kozakov, Dmitri Beglov, 2017, Journal of Computer-Aided Molecular Design.

Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.

D. Hall, S. McSweeney, I. Leiros, 2012, Acta crystallographica. Section D, Biological crystallography.

Ligand deconstruction: Why some fragment binding positions are conserved and others are not

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Proceedings of the National Academy of Sciences.

The mechanism of iron uptake by transferrins: the X-ray structures of the 18 kDa NII domain fragment of duck ovotransferrin and its nitrilotriacetate complex.

D. Hall, R. W. Evans, P. Lindley, 2002, Acta crystallographica. Section D, Biological crystallography.

Noncanonical FK506-Binding Protein BDBT Binds DBT to Enhance Its Circadian Function and Forms Foci at Night

D. Hall, J. Price, B. Agyekum, 2013, Neuron.

Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2010, Proteins.

The three-dimensional structure of a Plasmodium falciparum cyclophilin in complex with the potent anti-malarial cyclosporin A.

M. Berriman, A. Fairlamb, D. Hall, 2000, Journal of molecular biology.

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

INSIGHT INTO CHIRAL DISCRIMINATION, MECHANISM, AND SPECIFICITY OF CLASS II ALDOLASES*

D. Hall, W. Hunter, C. Bond, 2002 .

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

FTMAP: extended protein mapping with user-selected probe molecules

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2012, Nucleic Acids Res..

Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1

D. Stuart, D. Hall, J. Grimes, 2014, Acta crystallographica. Section D, Biological crystallography.

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Bioinform..

Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication

S. Vajda, R. Dingledine, D. Kozakov, 2011, Journal of Virology.

Minimal ensembles of side chain conformers for modeling protein–protein interactions

Roland L Dunbrack, Roland L. Dunbrack, Dima Kozakov, 2012, Proteins.

The ClusPro web server for protein–protein docking

Kathryn A. Porter, S. Vajda, D. Kozakov, 2017, Nature Protocols.

Sampling and scoring: A marriage made in heaven

Dima Kozakov, Sandor Vajda, David R. Hall, 2013, Proteins.