• Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. (wikipedia.org)
  • Rigorous introduction to the principles of macromolecular crystallography, aimed at students who are planning to carry out structural studies involving X-ray crystallography or who want to obtain in-depth knowledge for critical analysis of published crystal structures. (yale.edu)
  • This laboratory course provides hands-on training in the practical aspects of macromolecular structure determination by X-ray crystallography. (yale.edu)
  • In facts, often limitations in the availability of high-quality samples for X-ray crystallography call for the use of lower-resolution techniques like cryo-EM, where a compelling reconstruction of the structure of the complex requires the combined use of advanced computational techniques. (cecam.org)
  • The make-up and complexity of these molecular machines present perfect problems for structural biology and many of the protein components of these machines have been examined using X-ray crystallography or cryo-Electron Microscopy. (diamond.ac.uk)
  • Macromolecular Crystallography (MX) at Diamond reveals the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function. (diamond.ac.uk)
  • The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. (iucr.org)
  • These techniques are replacing x-ray crystallography for the determination of protein structure. (keywen.com)
  • We have developed a method for solving structures of homomeric coiled-coils with X-ray crystallography using denovo models, phasing and automatic model building. (lu.se)
  • http://www.ccp4.ac.uk/ ) is a suite of software for macromolecular X-ray crystallography. (lu.se)
  • Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. (wikipedia.org)
  • MMDB and VAST+: tracking structural similarities between macromolecular complexes. (nih.gov)
  • A fundamental reason is that the functional units of the cell are large macromolecular complexes, such as the ribosomes, proteasomes, or metabolons, whose detailed structure and dynamics are in many cases unknown. (cecam.org)
  • A clear understanding of protein-protein interactions, both for stable complexes and for transient ones, would therefore mark a major step forward, and it would have enormous consequences for designing new strategies of therapeutic intervention in diseases like cancer. (cecam.org)
  • Docking algorithms must therefore account for flexibility in order to allow predicting the structure of native complexes, but due to the computational cost typically only a limited flexibility is included [2,3]. (cecam.org)
  • The team showed that the structures of the variable region of two different TssA subunits were completely unrelated and they could assemble into distinctly different multisubunit complexes in terms of their size and geometry. (diamond.ac.uk)
  • CAPRI (Critical Assessment of PRediction of Interaction) is a community wide experiment designed to test methods to predict the structure of macromolecular complexes based on the known structure of their components ( http://www.ebi.ac.uk/msd-srv/capri/ ). (bioexcel.eu)
  • In recent years, Protein-peptide, protein-RNA complexes, and designed complexes for which affinity had to be predicted along with structure, have also been CAPRI targets. (bioexcel.eu)
  • But the realm of methods for predicting the structures of multi-component macromolecular complexes has significantly expanded in recent years. (bioexcel.eu)
  • With the exploding landscape of available protein sequences it has become possible to model the structures of individual proteins with increasing accuracy from sequence information alone and these models could soon be used as building blocs to assemble larger macromolecular complexes, using computation methods and additional experimental clues. (bioexcel.eu)
  • In this experiment members of the CASP community predicted the structures of the individual protein components, whereas members of the CAPRI community predicted the structures of the complexes formed by these components using classical docking methods or extrapolating from the structures of related complexes already deposited in the PDB. (bioexcel.eu)
  • Structure and properties of proteins, nucleic acids, and their complexes. (keywen.com)
  • Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. (researchgate.net)
  • The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. (researchgate.net)
  • Computational tools to study RNA-protein complexes. (ncbs.res.in)
  • The course comprises molecular biology of genes, proteins, multicomponent protein complexes, and other biomolecules that provide structure and perform the organism's functions. (lu.se)
  • genome informatics focuses on the development and application of algorithms and software for analysis of large sets of data, e.g. sequence sets and transcriptome data. (uni-hamburg.de)
  • There is a gap between our detailed knowledge of macromolecules present in many organisms, as provided by genome sequencing, and our scarce comprehension of the function of biological systems. (cecam.org)
  • GOLD provides the largest available and most detailed monitoring of genome sequencing projects. (fenteany.com)
  • Primary and secondary databases in areas of biology, genetics, pharmaceutical science and biomedical science including gene and protein sequence databases, 3-D structure databases, genome databases and disease databases. (londonmet.ac.uk)
  • Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. (ketabdownload.ir)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • Bioinformatics describes the computational analysis of genomes and macromolecular structures on a large scale. (yale.edu)
  • Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily. (nature.com)
  • Structural bioinformatics concentrates on model building and numerical simulation in areas such as protein or RNA structure and design of new molecules. (uni-hamburg.de)
  • Among contemporary bioinformatics concerns are reliable computational interpretation of a wide range of experimental data, and the detailed understanding of the molecular apparatus behind cellular mechanisms of sequence information. (re3data.org)
  • A course covering sequence bioinformatics, 3D macromolecular structure, and more, with impressive student projects displayed. (umass.edu)
  • The bioinformatics problem is simple to state: LMs are too short (and the information content too poor) to be statistically significant in protein sequence searches. (insulin-receptor.info)
  • However, useful advances are now being made in the bioinformatics tools that address the amazing modularity of eukaryotic regulatory proteins. (insulin-receptor.info)
  • As one of the founders of the field of bioinformatics, I have explored applications of computational techniques to a wide variety of biological problems, including protein structure, macromolecular sequence analysis, combinatorial chemistry and managing the enormous biomedical literature. (cuanschutz.edu)
  • With her team at the Free University of Brussels she then used molecular simulations and bioinformatics approaches to investigate the role of local interactions in stabilizing the native state of proteins, protein structure prediction, protein folding, and fold recognition. (bioexcel.eu)
  • Together with her teams at the Free University of Brussels, the European Bioinformatics Institute in Hinxton, UK, and at the Hospital for Sick Children in Toronto, they also developed efficient procedures for computational protein design, for simulating protein interactions and conformational changes, and for analysing protein interactions networks and cellular pathways. (bioexcel.eu)
  • CBS Prediction Servers - Nucleotide and amino acid sequence-based bioinformatics tools for structure and function prediction. (fenteany.com)
  • Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)
  • Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
  • 2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. . (ncbs.res.in)
  • With the help of various forms of mass spectrometry, synchrotron radiation, protein production & labelling, and bioinformatics, our facilities provide the opportunity to study protein structure and dynamics, molecular probes and drug design. (lu.se)
  • SCOP , Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. (berkeley.edu)
  • Key features are: Integrated MUSCLE alignment tool, Integrated HMMER2 package, OpenGL viewer for PDB macromolecular structures, and Workflow Designer to create and execute custom computational workflows. (bestfreewaredownload.com)
  • ClustalW - '[A] general purpose multiple sequence alignment program for DNA or proteins. (fenteany.com)
  • Application of online servers to sequence alignment and analysis of gene and protein databases, RNA structure prediction, molecular modelling and phylogenetic classification and pharmacogenomics analysis. (londonmet.ac.uk)
  • SEquence-structure alignment with 123D+ server. (keywen.com)
  • The structure of the molecules can be incorporated in the alignment. (keywen.com)
  • The input to the program was the alignment between the target sequence and template structure(s). (keywen.com)
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)
  • Uses Bio.Sequencing.Ace internally clustal The alignment format of Clustal X and Clustal W. See also the Bio.Clustalw module. (bugaco.com)
  • Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. (wikipedia.org)
  • Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid. (wikipedia.org)
  • The nature of the chemical bond and the structure of molecules and crystals. (uni-marburg.de)
  • BioViz Studio from Dark Star Systems is a web-based tool to help scientists create beautiful short videos of proteins and other molecules. (rcsb.org)
  • An app for the iPhone/iPad and Android that lets you browse protein, DNA, and drug molecules in 3D. (rcsb.org)
  • The major theme will be devoted to describe and analyze the molecules of life, light microscopy, fine cell structure and function, cell membranes structure and function, cell division and staining procedures. (uaeu.ac.ae)
  • However, when the adaptive process goes continuously during the many generation, the population of cells can use a special genetic mechanisms for the adaptation to 2 H 2 O. For example, mutations of geens can be resulted in amino acid replacements in molecules of proteins, which in turn could cause a formation of a new isoenzymes, and in the special cases - even the anomal working enzymes of a newer structure type. (o8ode.ru)
  • The module will examine applications of modelling with emphasis on understanding the interactions between proteins and other molecules of biological or synthetic origin. (londonmet.ac.uk)
  • Structure: an assortment of carbon molecules in a non-crystalline, irregular, glassy state. (keywen.com)
  • KGNMOL, ab initio electronic structure calculations for large molecules. (keywen.com)
  • UGENE provides customizable tools for visualization, analysis, annotation of genetic sequences. (bestfreewaredownload.com)
  • The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. (re3data.org)
  • 2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)
  • Deciphering protein–protein interactions. (crossref.org)
  • This may mean distilling information from a biological database or predicting properties of a macromolecule such as its structure or interactions. (uni-hamburg.de)
  • In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. (biomedcentral.com)
  • We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. (nih.gov)
  • Shoshana J. Wodak , earned her PhD at Columbia University, New York, under the supervision of Cyrus Levinthal, who was developing what were then the first and most powerful computational and graphics tools for modelling proteins and protein interactions. (bioexcel.eu)
  • Importing and implementing many of these tools to Belgium and France in the late seventies (with crucial support from CECAM (Centre pour le Calcul Atomique et Moléculaire) in Paris, and EMBO), she developed, in collaboration with Joel Janin, the first docking algorithms for the prediction of protein-protein interactions and one of the first procedures for defining structural domains from the atomic coordinates of proteins. (bioexcel.eu)
  • Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. (ketabdownload.ir)
  • Our facilities provide the opportunity to study protein structure, molecular probes and drug design, system biology and molecular interactions in cells and tissues. (lu.se)
  • A continuation of MB&B 600a that considers the chemistry and metabolism of nucleic acids, the mechanism and regulation of protein and nucleic acid synthesis, and selected topics in macromolecular biochemistry. (yale.edu)
  • Molecular Toolkit - Utilities to analyze and manipulate nucleic acid and protein sequences. (fenteany.com)
  • EBI Services - Access to nucleic acid, protein and macromolecular structure databases, including the EMBL-Bank database. (fenteany.com)
  • Refinement of macromolecular structures by the maximum-likelihood method. (pdbwiki.org)
  • Structure determination and refinement of human alpha class glutathione transferase A1-1. (keywen.com)
  • Motivation The goal of protein structure refinement is to enhance the precision of predicted protein models, particularly at the residue level of the local structure. (researchgate.net)
  • In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
  • Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
  • How to Measure the Similarity Between Protein Ligand-binding Sites. (uni-marburg.de)
  • The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)
  • 2.There is a known phenomenon, called "induced fit", whereby a target protein undergoes conformational changes upon ligand binding. (cecam.org)
  • Identification of protein-ligand binding sites is one of the most challenging tasks in drug discovery and design. (researchgate.net)
  • Recent advances in machine learning community, particularly deep learning, inspired considerable research into deep learning-based methods for protein ligand binding site prediction (PLBP) and have achieved promising results. (researchgate.net)
  • By Design meetings are 1-day symposium focusing on benefits of computer-aided ligand and structure-based drug design techniques for medicinal chemists, or methods in early stage biologics design. (chemcomp.com)
  • DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity. (ncbs.res.in)
  • Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. (wikipedia.org)
  • Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. (wikipedia.org)
  • The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. (wikipedia.org)
  • In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. (wikipedia.org)
  • Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da. (wikipedia.org)
  • The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
  • Class III HCPs differ from class I/II HCPs in the middle section of their primary amino acid structures (Supplementary Fig. 2 ) 25 . (nature.com)
  • Protein folding is thus the physico-chemical process by which a polypeptidic chain undergoes a structural change from an ensemble of coil like structure up to the unique structure encoded in its amino-acid sequence. (cea.fr)
  • However, unlike the other components of the harpoon, there are distinct variants of the TssA protein that contain radically different amino acid sequences at one end of the protein. (diamond.ac.uk)
  • The research team started by doing an analysis of the amino acid composition of four different TssA proteins. (diamond.ac.uk)
  • The essence of their function is usually embodied in the linear amino acid sequence and is not dependent on the tertiary structural context. (insulin-receptor.info)
  • In ICM, the amino acid sequence of the target was tethered to the parent structure. (keywen.com)
  • H3N2 viruses continue to ding to specific amino acids of the HA protein that are drift from the vaccine strain and may remain as the domi- directly involved in the divergence of antigenically distinct nant strains during the 2005-2006 influenza season. (cdc.gov)
  • A program for homology protein structure modeling by satisfaction of spatial restraints. (keywen.com)
  • In the last decade, the Center for Biological Sequence Analysis has produced a large number of computational methods, which are offered to others via WWW servers. (re3data.org)
  • A crucial problem that advanced computational approaches could solve is that of specificity: how are biologically unique connections made between proteins taken from a wealth of thousands of possible partners? (cecam.org)
  • Computational methods for biological sequence, structure and systems analysis. (jnu.ac.in)
  • 172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)
  • Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides. (wikipedia.org)
  • Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (wikipedia.org)
  • Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. (biomedcentral.com)
  • Many chromatin-associated proteins contain two sequence motifs rich in phenylalanine/tyrosine residues of unknown function. (diamond.ac.uk)
  • Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. (nature.com)
  • 2009. Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. Canadensis. (icr.org)
  • Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. (wikipedia.org)
  • This graduate course introduces the theory and application of biochemical and biophysical methods to study the structure and function of biological macromolecules. (yale.edu)
  • Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, queries, macromolecules and reactions for all operating systems, web pages and custom applications. (rcsb.org)
  • While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. (iucr.org)
  • For complicated structures, such as those of biological macromolecules, suitable initial models are built to fit electron-density distributions from Fourier syntheses, which require phase angles as well as the diffraction amplitudes. (iucr.org)
  • We proposed that a cell theoretically could in principle synthezise a big number of forms of [ 2 H]labeled macromolecules with somewhat different structures and conformations, so that a cell could easily select a preferable one from al these species in a course of adaptation to 2 H 2 O, that is the best suitable namely for that conditions. (o8ode.ru)
  • It is possible also to assume, that the macromolecules realize the special mechanisms, which promote a stabilization of their structure in 2 H 2 O and the functional reorganization for best working in 2 Н 2 О. (o8ode.ru)
  • siRNA Database - [A] comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms. (fenteany.com)
  • Many of the yeast subunits are homologs to proteins in higher organisms that are found associated with specific nuclear receptors such as THYROID HORMONE RECEPTORS and VITAMIN D RECEPTORS. (bvsalud.org)
  • Secondary structure element (SSE) identification from volumetric protein density maps is critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM). (researchgate.net)
  • This module aims to provide familiarity with the primary databases and common software packages used to analyse DNA, RNA and protein sequence, expression and structure, within and across genomes. (londonmet.ac.uk)
  • CBS offers Comprehensive public databases of DNA- and protein sequences, macromolecular structure, g ene and protein expression levels, pathway organization and cell signalling, have been established to optimise scientific exploitation of the explosion of data within biology. (re3data.org)
  • FASTA - 'Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. (fenteany.com)
  • The module uses online databases and software to extract, analyse and interpret DNA and protein sequences and to model structures of proteins. (londonmet.ac.uk)
  • SciVision - Databases , molecular modeling , and structure-activity relationship software for Windows. (keywen.com)
  • In addition to infrastructures for bioimaging, protein and genes & cells, we also provide other resources e.g., databases, networks and specialized labs. (lu.se)
  • Genomics describes the determination of the nucleotide sequence and many further analyses to discover functional and structural information on all the genes of an organism. (yale.edu)
  • Wah Chiu , of Baylor College of Medicine, gave the keynote lecture, entitled Protein Fold Determination of Large Macromolecular Assembly from Electron Cryomicroscopy and Sequence Threading . (stanford.edu)
  • Atomic structure determination is prominent among these, and is arguably pre-eminent. (iucr.org)
  • Forum for 3D macromolecular structure determination. (keywen.com)
  • Advanced spectroscopic techniques for structure and determination in organic chemistry . (keywen.com)
  • Crystal and molecular structure determination. (keywen.com)
  • Many biological processes are controlled by large multi-component protein assemblies, the size and complexity of which typically precludes the determination of their high-resolution structures. (lu.se)
  • Our goal is to use high-resolution structural modeling techniques guided by constraints taken from lower resolution experimental data to generate structural models of important biological protein assemblies for which high resolution structural determination is unfeasible. (lu.se)
  • Previous work in this area has been on modeling the assembly structure of the type III secretion system and prediction of the high-resolution structures of homo-oligomeric proteins using limited experimental data from Nuclear Magnetic Resonance (NMR) in order to speed up the process of structure determination. (lu.se)
  • Below is a non-exhaustive list of in-house infrastructures that are categorized into three overarching themes: bio-imaging, proteins, genes & cells and other resources. (lu.se)
  • Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
  • There are four distinct classes of ESBLs, termed A, B C and D based on specific sequence motifs and hydrolytic mechanism in Ambler classification system. (biomedcentral.com)
  • Using the links, experts can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation. (insulin-receptor.info)
  • INTRODUCTION Linear motifs (LMs) are short elements embedded within larger protein Rabbit polyclonal to ZFP161 sequence segments that operate as sites of regulation (1C5). (insulin-receptor.info)
  • These so-called FYRN and FYRC motifs are also found in transforming growth factor beta regulator 1 (TBRG1)/nuclear interactor of ARF and MDM2 (NIAM), a growth inhibitory protein that also plays a role in maintaining chromosomal stability. (diamond.ac.uk)
  • Following the synthesis by the ribosome, to carry out its biological function, a protein much fold into a single, well defined conformational state: the native state. (cea.fr)
  • Macromolecular synthesis (chromosome structure, cell division and its control). (lu.se)
  • Sequence-structure alignments Sequence-structure alignments were generated and tested both at the sequence level as well as at the 3D level. (keywen.com)
  • Multiple sequence alignments, (HI) assay and postinfection ferret antisera (11). (cdc.gov)
  • In favorable circumstances, which are not at all atypical, the number of unique reflections in the diffraction from a crystal exceeds the number of parameters needed to define its atomic structure, often manyfold overdeterminatively. (iucr.org)
  • However, since the atomic parameters relate nonlinearly to diffraction patterns, structure solution requires having an initial model within the radius of convergence of a minimization procedure that can relate the atomic model to the diffraction data. (iucr.org)
  • An X-ray diffraction study established the structure shown. (keywen.com)
  • Currently we are working with development of methods to determine structures of fibrillar proteins by a combination of structure modeling and X-ray fiber diffraction interference. (lu.se)
  • Other sources of experimental information include X-ray diffraction, biotinylation, sequence mutation and deletion, solution binding and chemical cross-linking data. (lu.se)
  • In addition, structural as well as functional aspects of the different classes of membrane proteins are discussed along with an outline of experimental approaches used to achieve an understanding of membrane protein structure and function at a molecular level. (yale.edu)
  • Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. (uni-marburg.de)
  • Unlike many other groups in the field of biomolecular informatics, Center for Biological Sequence Analysis directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. (re3data.org)
  • Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. (biomedcentral.com)
  • The use of Hidden Markov Models for functional identification of proteins has been pioneered through the development of HMM-ModE. (jnu.ac.in)
  • Functional states of the sodium channel (closed, open, and inactivated) and their structure help to understand the cardiac regulation processes. (bvsalud.org)
  • Resistance against β-lactam agents can occur via (i) mutation or expression of alternative penicillin-binding proteins (PBPs) as the drug target, (ii) downregulation of porins to reduce the bacterial permeability against β-lactams, (iii) over-expression of efflux systems which are membrane transport proteins to export drug substrates and (iv) production of β-lactamases that hydrolyze the β-lactam amide [ 6 ]. (biomedcentral.com)
  • New research sheds light onto how different bacterial species can build complex nano-harpoons with different protein building blocks. (diamond.ac.uk)
  • Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C400H620N100O120P1S1. (wikipedia.org)
  • An in-depth analysis of macromolecular structure and its elucidation using modern methods of structural biology and biochemistry. (yale.edu)
  • These areas are presented together with modern methods for analysis of macromolecular associations and dynamic properties. (yale.edu)
  • Computer Methods for Macromolecular Sequence Analysis. (berkeley.edu)
  • The ASTRAL compendium for sequence and structure analysis. (berkeley.edu)
  • Unipro UGENE for Linux is a free visual software solution for DNA and protein sequence analysis. (bestfreewaredownload.com)
  • Methods that improve small molecule docking scores, cheminformatics using data-mining methods, simulations of macromolecular systems and analysis of high-throughput data from biological experiments is the current focus of the lab in this area. (jnu.ac.in)
  • Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator. (ox.ac.uk)
  • Fur controls a wide variety of basic physiological processes including iron uptake systems and the expression of exotoxin A. Here, we present the first crystal structure of Fur from P. aeruginosa in complex with Zn2+ determined at a resolution of 1.8 A. Furthermore, X-ray absorption spectroscopic measurements and microPIXE analysis were performed in order to characterize the distinct zinc and iron binding sites in solution. (ox.ac.uk)
  • The mdxvu program is a molecular dynamics and molecular structure analysis code. (keywen.com)
  • The use of genetic engineering and modern techniques such as transcriptomics, proteomics and sequence analysis are included in the course. (lu.se)
  • The 2003-2004 influenza season was severe in terms of ducted a molecular analysis of the HA1 region of the HA its impact on illness because of widespread circulation protein. (cdc.gov)
  • measures distances and angles, superimposes structures, calculates RMSD between atom coordinates, structurally aligns chains, and displays dynamics trajectories. (rcsb.org)
  • Uses Bio.PDB.MMCIFParser to determine the (partial) protein sequence as it appears in the structure based on the atomic coordinates. (bugaco.com)
  • Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
  • Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. (iucr.org)
  • Static electric field strengths of 0.001 V/nm and 0.002 V/nm induced conformational changes in the protein but had no significant effect on its surface properties. (mdpi.com)
  • Induced fit phenomenon occurs also when two proteins associate, i.e. both of them undergo conformational changes, so that the structure of the complex is not equivalent to rigid composition of two proteins. (cecam.org)
  • Upon binding, proteins and small-molecule ligands can undergo significant conformational changes, as schematized by the "induced fit" and "conformational selection" paradigms [1]. (cecam.org)
  • NEBCutter - 'This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. (fenteany.com)
  • To address the first problem, we need scientists who develop methods for estimating changes in protein stability of binding upon mutations. (cecam.org)
  • Like CASP, it has greatly fostered the development of novel methods, like CASP, its continuation depends on the willingness of structural biologists to offer unpublished experimental structures as targets. (bioexcel.eu)
  • Current methods primarily rely on the availability of an existing atomic structure for fitting or a homologous template structure for modeling. (researchgate.net)
  • We have developed methods to predict the structure of homomeric coiled-coils, predict oligomerization state and denovo phasing of crystal structures of coiled-coils. (lu.se)
  • In affected indivi- chemicals possessing the ability to react with duals, it has a serious impact on their quality of proteins, and hence these methods do not esti- life. (cdc.gov)
  • The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)
  • Influence of macromolecular crowding on protein stability. (cea.fr)
  • A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. (biomedcentral.com)
  • Rational design of protein structure, activity, and stability. (keywen.com)
  • graphically shown within a Club Code format, which also displays known instances from homologous proteins through a novel Instance Mapper protocol based on PHI-BLAST. (insulin-receptor.info)
  • Open Source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials. (rcsb.org)
  • Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet. (keywen.com)
  • Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • Reads the contig sequences from an ACE assembly file. (bugaco.com)
  • A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. (iucr.org)
  • It is a slow and labor-intensive task to manually build protein structures from experimental electron density maps, therefore, machine learning approaches have been proposed to automate this process. (researchgate.net)
  • In this review, we consider some of the theoretical aspects of protein haptenation, how mechanisms of protein haptenation can be investigated experimentally and how we can use such knowledge in the development of novel, alternative approaches for predicting skin sensitization potential in the future. (cdc.gov)
  • It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR). (keywen.com)
  • It will also develop informatic skills for extracting, analysing and presenting data to extract biological knowledge and students will apply the principles of macromolecular, and in particular protein, structure to the building f molecular models using modelling and graphics software. (londonmet.ac.uk)
  • Principles of protein structure A course using internet. (keywen.com)
  • This macromolecular assembly comprises more than 20 conserved proteins that form a series of ring-like structures and a needle-shaped protrusion, which allows the transport of proteins into a host cell. (lu.se)
  • When the structure of the interacting proteins is known, either from experiments or from modeling, several docking algorithms are available which attempt to predict the geometry of the complex. (cecam.org)
  • Research has shown that the entire system consists of a protein complex that forms a large chamber that is anchored into the membrane. (diamond.ac.uk)
  • A CAPRI target is an unpublished crystal, NMR or high resolution cryo-EM structure of a protein-protein complex, communicated on a confidential basis by their authors to the CAPRI management. (bioexcel.eu)
  • Macromolecular complex annotations are imported from the Complex Portal . (yeastgenome.org)
  • HN - 2008 BX - Lateral Sinus MH - Atrial Septum UI - D054087 MN - A07.541.459.249 MS - The thin membrane-like muscular structure separating the right and the left upper chambers (HEART ATRIA) of a heart. (bvsalud.org)
  • The same is true for the problem of interpreting the dynamics of macromolecular aggregates from NMR spectroscopy, especially in the presence of natively unstructured proteins. (cecam.org)
  • Furthermore, several predictive tools for identifying natively disordered protein segmentsthe main harbour for LMs (28C30)have become available (31,32), complementing the more established globular domain resources Pfam, SMART, PROSITE and InterPro (33C36). (insulin-receptor.info)
  • A protein contains at least one long polypeptide. (wikipedia.org)
  • MOLGEN for automated structure elucidation. (keywen.com)
  • classification of large macromolecular structures in the structural classification of proteins-extended database. (berkeley.edu)
  • How the binding of small ligands like drugs affects the interaction patterns and thus the function of large macromolecular aggregates? (cecam.org)
  • The study of hydrogen bond evolution during the course of simulation revealed that the root mean square deviation, radius of gyration and secondary structure formation, all depend significantly on the number hydrogen bonds formed. (mdpi.com)
  • The European Ribosomal RNA Database - Ribosomal RNA (rRNA) sequence data listed by organism, secondary structure prediction programs and other software, links to related sites. (fenteany.com)
  • Protein secondary structure prediction based on position-specific scoring matrices. (keywen.com)