Evaluation of protein structure. Medical search. Frequent questions

The structures indicated that MORN repeats can mediate homotypic interactions, and can function as both dimerisation and oligomerisation devices. (biorxiv.org)
This makes it important to predict which residues participate in protein-protein interactions using only sequence information. (nih.gov)
Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
The University of Missouri will develop deep learning methods to predict inter-protein amino acid interactions and build three-dimensional structures of protein complexes, which are useful for designing and engineering protein molecules important for renewable bioenergy production. (energy.gov)
Protein-DNA interactions are essential for many biological processes. (biomedcentral.com)
2015. Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with its Metal Ion Effectors and DNA Binding Site. (middlebury.edu)
For the evaluation of the accuracy and reliability of the model in structure‑based drug design strategies, the crystal structure of the hepatitis C virus (HCV) helicase was used, complexed with a single‑stranded RNA, a key molecule for the establishment of interactions with a future inhibitor of the SPONV helicase. (spandidos-publications.com)
Our research laboratory focuses on understanding the functionality of different meat proteins and their interactions with various plant proteins. (uoguelph.ca)
The appointed student will be involved in ongoing research on the structure formation of hybrid meat and plant proteins, and interactions these proteins undergo during processing (e.g., hydration, heat induced gelation). (uoguelph.ca)

Proteins in cells interact and form complexes to carry out various biological functions such as catalyzing biochemical reactions. (energy.gov)
The team will use the deep learning methods it develops to construct green algae protein complexes that play important roles in biomass and biodiesel production. (energy.gov)
The technology and predicted structures of protein complexes will become valuable tools and resources for advancing U.S. bioenergy production and research. (energy.gov)
Protein complexes perform a diversity of functions in natural biological systems. (mdpi.com)
While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. (mdpi.com)
Coming to peace with protein complexes? (uu.nl)
They rely on thousands of protein complexes that form the executive machinery underlying biological processes, from DNA replication to protein degradation through metabolism. (uu.nl)
This is, however, not a trivial task and there is a large gap between the number of complexes identified by large-scale proteomics efforts and those for which high-resolution 3D experimental structures are available. (uu.nl)
Exploration of AlphaFoldDB, AlphaFold2 prediction of structures of single proteins and small complexes, FoldSeek for finding similar folds in other proteins, structure visualization with PyMol and Mol* Viewer, evaluation of structure reliability. (lu.se)

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. (plos.org)
His research spans a wide range, from the quantum chemistry of small molecules and the spectroscopic properties of proteins, to the application of state-of-the-art statistical and computer science methodology to problems in bioinformatics, drug design and sustainable chemistry. (nottingham.ac.uk)
Yet these proteins, which represent nearly 40 percent of all known proteins, including receptors, channels, and signaling molecules, are essential for cell communication and their malfunctions are implicated in many diseases. (the-scientist.com)
When Stevens tried to crystallize his GPCR, he found that cholesterol molecules were necessary for crystal formation, and from the structure, showed that cholesterol also acted as glue between the dimeric receptor molecules. (the-scientist.com)
Stevens collaborated with chemists to design new detergents, such as the cholate- based amphiphiles, that create smaller micelles, allowing the protein molecules to pack more closely and form better crystals. (the-scientist.com)
Of these, 4 800 structurally diverse, 'drug-like' molecules were selected for further evaluation. (europa.eu)
Two potent small molecules capable of disrupting the association of Nef with SH3 protein domains were identified and their chemical structures were used as models to generate additional inhibitors. (europa.eu)
It is important to obtain accurate three dimensional structures of molecules and proteins to understand and predict their function and behaviour. (lu.se)

High- and low-resolution structures of the MORN1 protein from Trypanosoma brucei and homologous proteins from the parasites Toxoplasma gondii and Plasmodium falciparum were obtained using a combination of macromolecular crystallography, small-angle X-ray scattering, and electron microscopy. (biorxiv.org)
Only those proteins are selected for which native structure is obtained via X-ray crystallography and are free from metal ions and prosthetic groups. (scfbio-iitd.res.in)
X-ray crystallography-still the only general method for solving the atomic structures of proteins of any size-has been hampered by the extreme difficulty of preparing and crystallizing pure membrane proteins. (the-scientist.com)
The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. (iucr.org)
X-ray crystallography is the major technique to determine three dimensional structures of proteins. (lu.se)
In small-molecule crystallography, some of the shortcomings in the model have already been overcome, but in protein crystallography they still remain. (lu.se)
Therefore, we have adapted the Hirshfeld atom refinement from small-molecule crystallography to make it available also to protein crystallography. (lu.se)

Protein structure prediction attempts via comparative modeling or ab initio approaches involve generating various three dimensional atomic level models/conformations for the protein sequence, followed by their rapid assay for locating the most preferred native-like conformation characterized by the minimum most free energy. (scfbio-iitd.res.in)
Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. (sciencegate.app)
This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. (sciencegate.app)
Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. (sciencegate.app)
To predict the structure of protein from a primary amino acid sequence is computationally difficult. (sciencegate.app)
This chapter covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. (sciencegate.app)
Second, DeepSF, a method of applying deep convolutional network to classify protein sequence into one of thousands known folds. (sciencegate.app)
These predicted structures often have low sequence and structure similarity to known structures. (sciencegate.app)
They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
Additionally, it can be argued that the kinds of matches that RUPEE does return have more added value than the current state of the art in that with equal scores it is able to return results not biased toward a structure classification hierarchy such as SCOPe or sequence clusters such as the PDB-90. (biorxiv.org)
5 Another approach is to insert mutations that alter the protein sequence in a manner that stabilizes one particular conformation, and screen to find those that might rigidify otherwise flexible regions. (the-scientist.com)
Our work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction. (biomedcentral.com)
Those are sequence identity but several tertiary structures. (predictioncenter.org)
These channels are quite different in terms of structure, sequence and function and both have been regarded as important targets for drugs aimed at treating atrial fibrillation. (frontiersin.org)

AbstractProtein structure prediction is a long-standing unsolved problem in molecular biology that has seen renewed interest with the recent success of deep learning with AlphaFold at CASP13. (sciencegate.app)
Proteins represent the functional end-product within the central dogma of molecular biology [ 1 ]. (biorxiv.org)
Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. (iucr.org)
We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. (springer.com)
Now that the molecular structure determines its biological function, structural information is expected to provide insight on the binding mechanism of SSB or DSB. (biomedcentral.com)
The molecular dynamics simulations suggested that the top-ranked compounds (3c, 3g and 3i) have a substantial effect on the protein dynamics which alter the protein function and have stable attachment in the protein active pocket. (bvsalud.org)
Molecular dynamics simulations show overall stability and moderate changes in protein structure upon compound binding. (bvsalud.org)

Furthermore, quantum refinement was applied to settle the nature of the unusual bidentate ligand in V-nitrogenase and the protonation state of the MoFe cluster in Mo-nitrogenase when inhibited by CO. For a recent structure of Mo-nitrogenase, we showed that there is no experimental support for the suggestion that N 2 is bound to the MoFe-cluster and presented a more likely model. (lu.se)

Protein structure prediction and evaluation is one of the major fields of computational biology. (sciencegate.app)
Protein structure prediction is one of the most important scientific problems in the field of bioinformatics and computational biology. (sciencegate.app)
There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
Therefore, a computational method is required to annotate the DNA binding protein as DSB or SSB automatically. (biomedcentral.com)
Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv. (ncsu.edu)
The subcellular localization of a set of 8 hypothetically secreted/surface candidate proteins was experimentally assessed by cellular fractionation and immunoelectron microscopy (IEM) to determine the reliability of the computational methodology proposed here, using 4 secreted/surface proteins with experimental confirmation as positive controls and 2 cytoplasmic proteins as negative controls. (ncsu.edu)
Based on statistical learning methods, we obtained computational subcellular localization predictions that were experimentally assessed and allowed us to construct a computational protocol with experimental support that allowed us to identify a new set of secreted/surface proteins as potential vaccine candidates. (ncsu.edu)
Unfortunately, the design of drugs with multiple activities on a selected handful of different protein structures remains a significant experimental and computational challenge ( Konc, 2019 ). (frontiersin.org)

Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Truncating RAD21 variants are shown above, and missense mutations and in-frame deletions are shown below the protein representation. (springer.com)
Based on the structure, we performed integrative analysis of the cellular trafficking, protein thermostability, ATP hydrolysis, and the transport activity of representative mutations. (elifesciences.org)
By determining the cryo EM structure of human ABCD1 the study represents a valuable insight into its transport mechanism and the mechanistic basis for mutations causing the severe neurodegenerative disorder, X-linked adrenoleukodystrophy. (elifesciences.org)
The structure and functional studies of disease-causing mutations are solid and will appeal to the transporter and medical genetics communities. (elifesciences.org)
These isolates carried the mutations T2504A and C2534T in multiple 23S rRNA copies and 2 mutations leading to relevant amino acid substitutions in L3 protein. (cdc.gov)
Linezolid resistance in S. epidermidis has been attributed to specific 23S rRNA mutations (G2576U, G2447U, U2504A, C2534U, and G2631U) ( 5 , 6 ), cfr gene ( 7 ), or mutations in ribosomal proteins L3, L4, and L22 ( 7 ). (cdc.gov)
In 8 LRSE isolates representing all PFGE types, genes encoding the L3, L4, and L22 ribosomal proteins that factor in ribosome assembly were sequenced to identify mutations conferring linezolid resistance ( 6 ). (cdc.gov)
Other PMP22 gene mutations that lead to a reduction of PMP22 protein can also cause the condition. (medlineplus.gov)
All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)

Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. (biorxiv.org)
As such, understanding protein structure is a central goal within structural bioinformatics. (biorxiv.org)
In addition, some recent works such as [ 19 , 20 ] adopted structural information in other bioinformatics fields and the considerable performance gains indicate the huge potential of protein structural information. (biomedcentral.com)

MORN (membrane occupation and recognition nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. (biorxiv.org)
The challenges of crystallizing membrane proteins-and how they're being overcome Computer artwork of a G protein-coupled receptor in the lipid bilayer of a plasma membrane Medi-Mation Ltd / Photo Researchers Membrane proteins represent only a handful of the total number of protein structures defined to date. (the-scientist.com)
Membrane proteins represent only a handful of the total number of protein structures defined to date. (the-scientist.com)
The choice of detergent used to isolate membrane proteins can also have a profound effect on their ability to crystallize. (the-scientist.com)
Because many membrane proteins are expressed by multiple species, homologous genes should be tested and screened to identify proteins that are most amenable to crystallization. (the-scientist.com)
Similarly, removing the hydrophilic and flexible ends of a membrane protein can improve crystal formation. (the-scientist.com)
The translated polyprotein consists of three structural [capsid (C), membrane (M) and envelope (E)] and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). (spandidos-publications.com)
Adrenoleukodystrophy protein (ALDP) is responsible for the transport of very-long-chain fatty acids (VLCFAs) and corresponding CoA-esters across the peroxisomal membrane. (elifesciences.org)
The adrenoleukodystrophy protein (ALDP) or ABCD1 is an ABC transporter that participates in the transport of free very long-chain fatty acids and their CoA esters across the peroxisomal membrane. (elifesciences.org)
Phylogenetic analysis showed similar numbers of AQPs clustered in five distinct subfamilies including the plasma membrane intrinsic proteins (PIPs), the tonoplast intrinsic proteins (TIPs), the nodulin 26-like intrinsic proteins (NIPs), the small basic intrinsic proteins (SIPs), and the uncharacterized intrinsic proteins (XIPs). (biomedcentral.com)
Aquaporins (AQPs) are small (21-34 kD) integral membrane proteins, which form channels facilitating movement of water and other small solutes across the cell membrane. (biomedcentral.com)

The number of available protein structures still lags far behind the number of known protein sequences. (nih.gov)
We applied support vector machines to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. (nih.gov)
We have developed RUPEE, a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. (biorxiv.org)
Participants may bring their own protein sequences to work on during the hands on part of the course. (lu.se)

We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. (biomedcentral.com)
Given that the energy potentials are mainly derived from the predicted protein properties, the accuracy of the predicted protein properties, to a large extent, determines the quality of final predicted structures. (biomedcentral.com)
Knowledge-based methods, such as statstical potentials, for analyzing protein structures primarily consider the distances between pairs of bodies (atoms or groups of atoms). (purdue.edu)
Evaluation of different methods to calculated reduction potentials for heme proteins. (lu.se)

Histopathological evaluation and measurements of muscle strength were accompanied by analyses of expression for 12 488 known genes at four time points ranging from 6 h to 7 days after injury. (cdc.gov)
Only CI activated a set of genes associated with the repair of impaired proteins and structures including genes related to apoptosis, whereas FI uniquely activated gene sets involved in extensive inflammatory responses, tissue remodelling, angiogenesis and myofibre/extracellular matrix synthesis. (cdc.gov)

As compared with the original version, substantial improvements that have been incorporated to our software allow: (i) to compare quaternary structures, (ii) to deal with a list of pairs of structures, (iii) to know how druggable is the zone where similar 3D patterns are detected and (iv) to significantly reduce the execution time. (frontiersin.org)
Thus, the new algorithm achieves up to 353x speedup as compared to the previous sequential version, allowing the exploration of a significant number of quaternary structures in a reasonable time. (frontiersin.org)

In this study, the genome of Mycobacterium tuberculosis H37Rv was screened using Machine Learning tools that included feature-based predictors, general localizers and transmembrane topology predictors to identify proteins that are potentially secreted to the surface of M. tuberculosis, or to the extracellular milieu through different secretory pathways. (ncsu.edu)

Structure validation is a particularly important component of the structure determination pipeline as many protein structures have small structural errors (i.e. distorted bond lengths or angles, incompatible torsion angles, overlapping atoms) that are not easily detected by visual inspection. (wikipedia.org)
For most of its graphs and charts, PROSESS uses a simple RAG (red, amber, green) color scheme to indicate the quality of different structure parameters for the protein (as a whole), for different members of the structure ensemble, for specific residues and for specific atoms. (wikipedia.org)
Different shades of red indicate serious problems, different shades of yellow or amber indicate potential problems and different shades of green indicate that the protein model or its residues/atoms are free of problems. (wikipedia.org)
E el is the electrostatic contribution to the energy, E vdw is the van der Waals term, E hpb is the hydrophobic contribution and the summation runs over all the atoms of the protein [1-4] . (scfbio-iitd.res.in)
Proteins which are fragments or mutlimers, or having mismatches in the number of atoms between native and decoys are also skipped. (scfbio-iitd.res.in)
Fragment libraries contain rich structural information, including 1D structural properties such as secondary structure and torsion angles, and 2D structural properties such as distances and orientations between pairs of heavy atoms. (biomedcentral.com)

While developing and evaluating protein structure prediction methods, researchers may want to identify the most similar known structures to their predicted structures. (sciencegate.app)

CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. (plos.org)
The mycobacterial cell envelope has been implicated in the pathogenicity of tuberculosis and therefore has been a prime target for the identification and characterization of surface proteins with potential application in drug and vaccine development. (ncsu.edu)
This characterization provides context for defining benchmarks for the evaluation of NAMs for skin sensitization assessments. (nih.gov)
Functional and structural characterization of human adrenoleukodystrophy protein (ALDP). (elifesciences.org)

PROSESS can handle single-chain X-ray models, multi-chain X-ray models, single-chain NMR ensembles, multi-chain NMR ensembles of monomeric and multimeric proteins. (wikipedia.org)
Currently the program works only for monomeric globular proteins. (scfbio-iitd.res.in)

The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
In the meantime, the investigation results can help to annotate or refine the annotation of the proteins with known structures yet unknown or not fully understood functions. (biomedcentral.com)

The availability of protein three-dimensional (3D) structure is crucial for studying biological and cellular functions of proteins. (sciencegate.app)
SIRT1 is a protein associated with vital cell functions such as gene regulation, metabolism, ageing, and cellular energy restoration. (bvsalud.org)
Oxidant damage to cellular DNA, proteins (including the epigenome), and lipids can occur when reactive oxygen species escape cell antioxidant and repair mechanisms. (who.int)

Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation CHEMISTRY-A EUROPEAN JOURNAL. (nottingham.ac.uk)
Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. (mdpi.com)

First, DNSS2, a method for protein secondary structure prediction using one-dimensional deep convolution network. (sciencegate.app)

Other methods for structure validation (such as ProCheck, MolProbity, ResProx and VADAR) focus on measuring coordinate data, rather than experimental data, to assess the quality of the bond or torsion angle geometry. (wikipedia.org)
PROSESS is unique among structure validation servers in that it evaluates both coordinate quality and experimental data quality. (wikipedia.org)
Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. (biomedcentral.com)

Proteins : Struct Funct Genet Suppl 3, 171-176 (1999). (scfbio-iitd.res.in)

Deepened knowledge on the biophysical chemistry of proteins with emphasis on properties rather than methods. (lu.se)

In this study, to leverage the structural information provided by fragment libraries, we first directly extracted multiple structural properties from fragment libraries and proposed novel fragment-level metrics for evaluation. (biomedcentral.com)

In primitive land plants, two additional unique classes of AQPs, GlpF-like intrinsic protein (GIPs) and hybrid intrinsic proteins (HIPs) have been described and are presumed to have been lost in the course of evolution [ 12 ]. (biomedcentral.com)

Among the factors that contribute to the progression of HIV is Nef (Negative Regulatory Factor), a protein that promotes viral replication and facilitates immune evasion. (europa.eu)
Therefore, the present study proposes the three‑dimensional structure of the helicase/protease enzyme of SPONV through homology modeling, using the crystal structure of the Dengue virus‑4 helicase/protease of the same viral family as a template. (spandidos-publications.com)
The most crucial NS proteins are the viral helicase and the viral RNA-dependent RNA polymerase (RdRp) ( 2 ). (spandidos-publications.com)
The viral proteins are then transferred onto nitrocellulose paper and reacted with the patient's serum. (cdc.gov)
Positive and negative control serum specimens are run simultaneously to allow identification of viral proteins. (cdc.gov)
However, in a recent study, the protein with a mobility of 160 kilodaltons (kd) present in commercially available Western blots and in viral lysate antigen preparations was identified as a multimer of the gp41 protein (10,11). (cdc.gov)
Although the overall sensitivity and specificity of the Western blot for detection of antibodies to the various viral proteins are high, there has been substantial debate regarding the interpretive criteria. (cdc.gov)

An investigation of the methods and algorithms used to predict protein structure and a thorough knowledge of the function and structure of proteins are critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. (sciencegate.app)
To that end, this chapter sheds light on the methods used for protein structure prediction. (sciencegate.app)
With this resource, it presents an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction, giving unique insight into the future applications of the modeled protein structures. (sciencegate.app)
In this chapter, current protein structure prediction methods are reviewed for a milieu on structure prediction, the prediction of structural fundamentals, tertiary structure prediction, and functional imminent. (sciencegate.app)
Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. (iucr.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)
We employ different physical, chemical, biochemical, and optical methods to gain insight into the structure formation and its relation to texture and water binding (both essential for producing acceptable food products). (uoguelph.ca)
Automated methods to determine hydrogen positions in neutron crystal structures. (lu.se)

Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. (biomedcentral.com)
The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. (frontiersin.org)
that target them requires taking the step towards solving their three-dimensional structures. (uu.nl)

For example, serum biomarkers, such as high sensitivity C-reactive protein (hsCRP) and cytokine levels, predict progression of atherosclerosis and risk of stroke. (medscape.com)

In addition to its ability to validate structures using chemical shifts, PROSESS also checks many other protein structure parameters including covalent bond quality, non-covalent bond and atomic packing quality, torsion angle quality and NOE quality (i.e. measuring the model agreement with NOE-based distance restraints). (wikipedia.org)
Besides our approach to protein structure search, we introduce a polar plot for torsion angles that may have wider applicability in the study of protein structure. (biorxiv.org)
Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. (biomedcentral.com)

Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. (sciencegate.app)

With immuno-flowFISH they can analyse the leukaemia cells based on their surface protein structure, and then assess whether there are abnormal chromosomes inside the cell with fluorescence in situ hybridisation (FISH). (riotinto.com)

Chemical shifts are easily and very precisely measurable NMR observables that provide a great deal of information about protein structure and dynamics (see Protein Chemical Shift Prediction). (wikipedia.org)
Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. (plos.org)
Careful phenotyping is essential in interpreting consequences of RAD21 variants, and protein modeling and dynamics can be helpful in determining pathogenicity. (springer.com)

Although, the number of omic techniques is ever expanding, the most developed omics technologies are high throughput DNA sequencing, transcriptomics (focused on gene expression), epigenomics (focused on epigenetic regulation of gene expression), proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of metabolites, the metabolome). (who.int)

Thus the scoring function presented here can be utilized in conjunction with protein structure prediction methodologies such as ab initio or comparative modeling for bracketing native-like structures. (scfbio-iitd.res.in)
A parallel multi-objective ab initio approach for protein structure prediction. (ncsu.edu)
This work proposes a novel and suitable methodology to model protein structure prediction with atomic-level detail by using a parallel multi-objective ab initio approach. (ncsu.edu)

The results of this research provide insight into recent work regarding the physical chemistry of amino acids and their role in the structure, function and evolution of proteins. (purdue.edu)

Devising a scoring function that can mimic a free energy function and can distinguish between correct (native or native-like) structures from incorrect ones is a challenging task. (scfbio-iitd.res.in)
Over the past few years,there is a continuous progression in the ability of empirical potential functions and protocols in pinning down the native as the lowest energy structure, yet design of an energy function which shows 100% discrimination between the native and the decoys is not achieved. (scfbio-iitd.res.in)
The scoring function considers the non-bonded energy of a protein, expressed as a sum of three terms - electrostatics, van der Waals and hydrophobicity. (scfbio-iitd.res.in)
The empirical scoring function is validated on 69 proteins and their 61974 decoys, belonging to twelve different publicly available as well as our own build decoy sets. (scfbio-iitd.res.in)
Structure and relation to Function. (lu.se)

Following the evaluation of the model and the identification of motifs characteristic of the Flaviviridae family, data from previous publications on the treatment of HCV were incorporated, with the aim of detecting the ideal residues in the Spondweni model, which are similar to those of the HCV structure and are inhibitor targets. (spandidos-publications.com)

Third, CNNQA and DeepRank, two deep neural network approaches to systematically evaluate the quality of predicted protein structures and select the most accurate model as the final protein structure prediction. (sciencegate.app)
Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. (biorxiv.org)
A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. (iucr.org)
Although fragment libraries are extensively utilized in fragment assembly, the rich structural information has not yet been systematically analyzed and leveraged by other protein structure prediction approaches. (biomedcentral.com)

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)

Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. (iucr.org)

This enables improved modelling of high-resolution protein data. (lu.se)

With quantum refinement, it is possible to distinguish between different interpretations of the structure, e.g. the elemental composition or the protonation state, even from medium-resolution crystallographic data. (lu.se)

In response to the presence of certain activating substances, including oxidized LDL, monocyte chemoattractant protein 1 (MCP-1), interleukin (IL)-8, and platelet-derived growth factor (PDGF), leukocytes migrate into the wall of the artery (see the image below). (medscape.com)

The problem is a practical one: hydrophilic proteins, such as those in the cytoplasm, can form crystals in solution. (the-scientist.com)
Protein structure evaluation showed a hydrophilic aromatic/arginine (ar/R) selectivity filter (SF) in PIPs whereas other subfamilies mostly contained a hydrophobic ar/R SF. (biomedcentral.com)

Their project, Australia-Japan Collaboration to Improve the Identification of Blood Cancers with Immuno-flowFISH will conduct pre-clinical evaluation of a new diagnostic tool developed by Erber and Fuller for more precise targeting of blood and bone marrow cancers. (riotinto.com)

Table 1 lists the major structural proteins coded for by the HIV genome. (cdc.gov)

Chopping off the termini of proteins is a trick long-used to make soluble cytosolic proteins more amenable to crystallization. (the-scientist.com)
The domains are Single domain protein with poorly integrated termini. (predictioncenter.org)

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)

The program displays the electrostatics, van der Waals and hydrophobic components as well as total energy of the protein (kcal/mol). (scfbio-iitd.res.in)

Anatomy2

Organisms6

Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment63

Psychiatry and Psychology1

Phenomena and Processes86

Disciplines and Occupations12

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Interactions11

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Membrane11

Sequences4

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Identify proteins1

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Evaluating protein structure1

Characterization4

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Peptides2

Secondary1

Experimental4

Suppl1

Biophysical1

Metrics1

Intrinsic1

Viral7

Methods8

Dimensional3

Predict1

Torsion3

Experimentally determined1

Analyse1

Dynamics3

Gene1

Initio3

Amino acids1

Function5

Residues1

Approaches4

Macromolecules1

Structural genomics1

High resolution protein1

Distinguish1

Substances1

Hydrophilic2

Identification1

Genome1

Termini2

Diffraction2

Hydrophobic1