Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures [PDF]
, 2003 We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device.
Bagci +50 more
core +2 more sources
Fundamentals of protein interaction network mapping
Molecular Systems Biology, 2015 Studying protein interaction networks of all proteins in an organism ("interactomes") remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases.
Jamie Snider +5 more
openaire +3 more sources
Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. [PDF]
PLoS ONE, 2012 Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of ...
Ching-Tai Chen +9 more
doaj +1 more source
A tractable genotype-phenotype map for the self-assembly of protein quaternary structure
, 2013 The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here we introduce a rich, intuitive, and biologically realistic genotype-phenotype (GP) map, that serves as a model of self-assembling biological ...
Ahnert, Sebastian E. +3 more
core +1 more source
Graph Theory and Networks in Biology [PDF]
, 2006 In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to ...
Mason, Oliver, Verwoerd, Mark
core +3 more sources
Revealing the structure of land plant photosystem II: the journey from negative‐stain EM to cryo‐EM
FEBS Letters, EarlyView.Advances in cryo‐EM have revealed the detailed structure of Photosystem II, a key protein complex driving photosynthesis. This review traces the journey from early low‐resolution images to high‐resolution models, highlighting how these discoveries deepen our understanding of light harvesting and energy conversion in plants.
Roman Kouřil
wiley +1 more source
Heterologous Expression and Purification of \u3cem\u3eVibrio proteolyticus (Aeromonas proteolytica)\u3c/em\u3e Aminopeptidase: A Rapid Protocol [PDF]
, 2009 Metalloaminopeptidases (mAPs) are enzymes that are involved in HIV infectivity, tumor growth and metastasis, angiogenesis, and bacterial infection. Investigation of structure–function relationships in mAPs is a prerequisite to rational design of anti-mAP
Bennett, Brian, Hartley, Mariam
core +1 more source
Solitonic Effects of the Local Electromagnetic Field on Neuronal Microtubules [PDF]
, 2007 Current wisdom in classical neuroscience suggests that the only direct action of the electric field in neurons is upon voltage-gated ion channels which open and close their gates during the passage of ions.
Georgiev, Danko +2 more
core +1 more source
Mapping the evolution of mitochondrial complex I through structural variation
FEBS Letters, EarlyView.Respiratory complex I (CI) is crucial for bioenergetic metabolism in many prokaryotes and eukaryotes. It is composed of a conserved set of core subunits and additional accessory subunits that vary depending on the organism. Here, we categorize CI subunits from available structures to map the evolution of CI across eukaryotes. Respiratory complex I (CI)
Dong‐Woo Shin +2 more
wiley +1 more source
The COOH terminus of the c-Abl tyrosine kinase contains distinct F- and G-actin binding domains with bundling activity [PDF]
, 1994 The myristoylated form of c-Abl protein, as well as the P210bcr/abl protein, have been shown by indirect immunofluorescence to associate with F-actin stress fibers in fibroblasts. Analysis of deletion mutants of c-Abl stably expressed in fibroblasts maps
Baltimore, David +5 more
core +4 more sources