33 Result(s)
within
Tom L Blundell
Life Sciences
-
Article
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryogenic electron microscopy (cryo-EM) ...
-
Article
Open AccessHuman DNA-dependent protein kinase activation mechanism
DNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. Using a DNA...
-
Article
Open AccessMycobacterium abscessus pathogenesis identified by phenogenomic analyses
The medical and scientific response to emerging and established pathogens is often severely hampered by ignorance of the genetic determinants of virulence, drug resistance and clinical outcomes that could be u...
-
Article
Open AccessA base measure of precision for protein stability predictors: structural sensitivity
Prediction of the change in fold stability (ΔΔG) of a protein upon mutation is of major importance to protein engineering and screening of disease-causing variants. Many prediction methods can use 3D structura...
-
Article
Dimers of DNA-PK create a stage for DNA double-strand break repair
DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent protein kinas...
-
Protocol
The Genome3D Consortium for Structural Annotations of Selected Model Organisms
Genome3D consortium is a collaborative project involving protein structure prediction and annotation resources developed by six world-leading structural bioinformatics groups, based in the United Kingdom (name...
-
Article
Dissection of DNA double-strand-break repair using novel single-molecule forceps
Repairing DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) requires multiple proteins to recognize and bind DNA ends, process them for compatibility, and ligate them together. We constructed...
-
Chapter and Conference Paper
Protein-Protein Interactions: Structures and Druggability
While protein-protein interfaces have promised a range of benefits over conventional sites in drug discovery, they present unique challenges. Here we describe recent developments that facilitate many aspects o...
-
Article
Open AccessPolyphony: superposition independent methods for ensemble-based drug discovery
Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the st...
-
Article
Open AccessThe crystal structure of fibroblast growth factor 18 (FGF18)
-
Article
Open AccessComprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database
Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization ...
-
Article
Open AccessOn the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture
The hydrogen bond patterns between mainchain atoms in protein structures not only give rise to regular secondary structures but also satisfy mainchain hydrogen bond potential. However, not all mainchain atoms ...
-
Article
Structural and functional constraints in the evolution of protein families
The process of protein evolution is balanced between Darwinian selection for functionally advantageous mutations and neutral evolution, in which acceptance of ...
-
Article
Open AccessStructural assembly of two-domain proteins by rigid-body docking
Modelling proteins with multiple domains is one of the central challenges in Structural Biology. Although homology modelling has successfully been applied for prediction of protein structures, very often domai...
-
Article
Open AccessComparative modelling by restraint-based conformational sampling
Although comparative modelling is routinely used to produce three-dimensional models of proteins, very few automated approaches are formulated in a way that allows inclusion of restraints derived from experime...
-
Article
Open AccessGenome bioinformatic analysis of nonsynonymous SNPs
Genome-wide association studies of common diseases for common, low penetrance causal variants are underway. A proportion of these will alter protein sequences, the most common of which is the non-synonymous si...
-
Article
Open AccessRapper tk: a versatile engine for discrete restraint-based conformational sampling of macromolecules
Macromolecular structures are modeled by conformational optimization within experimental and knowledge-based restraints. Discrete restraint-based sampling generates high-quality structures within these restrai...
-
Article
Is one solution good enough?
-
Article
Open AccessPROVAT – a versatile tool for Voronoi tessellation analysis of protein structures and complexes
-
Article
Crystal structure of an Xrcc4–DNA ligase IV complex
A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here ...
