Protein homology detection. Medical search. Frequent questions

In recent work we developed the first bioinformatic representation of protein dynamics, and are currently using this tool, in combination with earlier studies of the static physical properties of amino acid sequences, to elucidate basic mechanisms of protein folding. (rochester.edu)
We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.edu)
Global informatics and physical property selection in protein sequences. (rochester.edu)
Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
Beyond supersecondary structure: the global properties of protein sequences. (rochester.edu)
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (ncbs.res.in)
A straightforward comparison procedure using pairwise protein sequences similarities was suggested in Rankprot [26], in addition to distance-profile methods reported in [29]. (columbiagypsy.net)
To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. (biorxiv.org)
By using in silico tools, LipJG3 was related to the transporter protein sequences. (ugm.ac.id)
Since proteins are of varying lengths, there is a need for a means of representing protein sequences by a fixed-number of features. (metu.edu.tr)
Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and ß-sheets. (bvsalud.org)
Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
The Structural Classification of Proteins - extended ( SCOPe ) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst all proteins of known structure, along with resources for analyzing the protein structures and their sequences. (berkeley.edu)
A novel kernel function, stem kernel, for the discrimination and detection of functional RNA sequences using support vector machines (SVMs) is proposed. (elsevierpure.com)
This is because the string kernel is proven to work for the remote homology detection of protein sequences. (elsevierpure.com)
Comparison of the putative amino acid sequences of the ftsZ proteins showed similar homology. (bgu.ac.il)
A genome-wide survey for N-terminal signal sequences using bioinformatic tools (Psortb 2.0 and SignalP 3.0) combined with a strategy of the subtraction of lipoproteins and proteins containing multiple transmembrane domains yielded 116 secretory proteins. (cdc.gov)

The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. (biomedcentral.com)
Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis , and 708 protein structures and 7391 protein interactions for L. infantum . (biomedcentral.com)
The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. (biomedcentral.com)
3Dmapper: A New Tool for Mapping Genetic Variants to Protein Structures. (cbirt.net)
Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. (biomedcentral.com)
It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. (biomedcentral.com)
By Sep 2009, the PDB contained ~ 60,713 experimental protein structures that can be grouped into ~ 3500 families [ 2 ]. (biomedcentral.com)
However, these efforts are no where near in solving the 3 D structures of all the known proteins in any system. (biomedcentral.com)
In the absence of experimental structures, computational methods are used to predict 3 D protein models to provide insight into the structure and function of these proteins. (biomedcentral.com)
MODELLER is one of the most widely used tools for homology or comparative modeling of protein three-dimensional structures. (biomedcentral.com)
Meier, A. and Söding, J. (2015) Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. (mpg.de)
Such fold switching may have occurred over evolutionary history, but supporting evidence has been limited by the: (1) abundance and diversity of sequenced genes, (2) quantity of experimentally determined protein structures, and (3) assumptions underlying the statistical methods used to infer homology. (bvsalud.org)
SCOPe undertakes to provide interfaces and data to support all users of protein structure and evolutionary relationships, for research, education, and policy, at scales ranging from interactive exploration of relationships of proteins of interest, including nuances of their individual structures and variations, to comprehensive studies and methods that draw on the entirety of the protein universe. (berkeley.edu)
Furthermore, the potential application of the stem kernel is demonstrated by the detection of remotely homologous RNA families in terms of secondary structures. (elsevierpure.com)

The origin of the eukaryotic N- glycosylation pathway is not unique and less straightforward than previously thought: some basic components likely have proteoarchaeal origins, but the pathway was extensively developed before the eukaryotic diversification through multiple gene duplications, protein co-options, neofunctionalizations and even possible horizontal gene transfers from bacteria. (biomedcentral.com)
More than half of all eukaryotic proteins are glycoproteins, and 90 % of those are N- glycosylated [ 33 ]. (biomedcentral.com)
VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). (embl.de)
Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. (embl.de)
In recent years, however, evidence has emerged on numerous T6SS effectors that interact with related immunity proteins in a range of eukaryotic hosts. (preprints.org)

Alternative approach to protein structure prediction based on sequential similarity of physical properties. (rochester.edu)
Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. (biomedcentral.com)
We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. (biomedcentral.com)
These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. (biomedcentral.com)
Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
Our work is focussed on protein function and structure prediction, sequence search and assembly in metagenomics, transcription regulation, gene regulatory networks, and systems medicine. (mpg.de)
Söding, J. (2017) Big-data approaches to protein structure prediction. (mpg.de)

1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. (wikipedia.org)

The current work presents an alternative method for SVM-based protein classification. (columbia.edu)
Efficient use of unlabeled data for protein sequence classification: a comparative study. (uni-trier.de)
On the Role of Local Matching for Efficient Semi-supervised Protein Sequence Classification. (uni-trier.de)
Conotoxins thus offered the ideal protein group to test a new classification algorithm on. (columbiagypsy.net)
1.1 Related methods Several methods possess been suggested for protein homology detection and classification, whereby most of the successful methods were based on profile-sequence or profile-profile alignment. (columbiagypsy.net)
In addition, recent years possess witnessed remarkable overall performance enhancement in proteins classification stemming in the work of support vector devices (SVM) as a favorite statistical machine learning device [18,19]. (columbiagypsy.net)
We have developed the FunFam-MARC (Multidomain ARchitecture-based Clustering) protocol, which uses multi-domain architectures of protein kinases and specificity-determining residues for functional family classification. (bvsalud.org)
MOTIVATION: CATH is a protein domain classification resource that exploits an automated workflow of structure and sequence comparison alongside expert manual curation to construct a hierarchical classification of evolutionary and structural relationships. (bvsalud.org)
By providing a broad survey of protein folds and authoritative information about relatives of proteins, particularly those too ancient to be readily recognized from sequence, SCOPe is a framework for future research and classification. (berkeley.edu)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)

The problems of protein fold recognition and remote homology detection have recently attracted a great deal of interest as they represent challenging multi-feature multi-class problems for which modern pattern recognition methods achieve only modest levels of performance. (videolectures.net)
Currently, one of the most powerful such homology detection methods is the SVM-Fisher method of Jaakkola, Diekhans and Haussler (ISMB 2000). (columbia.edu)
Deep Learning Powers New Methods for Protein Remote Homology Detection and. (cbirt.net)
The SCOOP approach [30] regarded as common sequence matches between two Pfam HMM profile search results, and performed better than elaborated methods such as HHsearch in detecting protein superfamily relationship. (columbiagypsy.net)
We evaluated our methods both in generating accurate template-query alignment and protein threading. (biomedcentral.com)
Inspired by the success of non-linear models in TBM methods, we would like to study if we can improve TBM methods' model accuracy using more advanced neural network architecture such as deep residual network which has proven very successful in protein residue-residue contacts prediction. (biomedcentral.com)
Here, we overcome these barriers by applying multiple statistical methods to a family of ~600,000 bacterial response regulator proteins. (bvsalud.org)
Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)

We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. (rochester.edu)
Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum . (biomedcentral.com)
VeraChem's state of the art computational chemistry software is capable of protein-ligand and host-guest binding affinity prediction, fast calculation of accurate partial atomic charges for drug-like compounds, computation of energies and forces with empirical force fields, automatic generation of alternate resonance forms of drug-like compounds, conformational search with the powerful Tork distort-minimize algorithm, and automatic detection of topological and 3D molecular symmetries. (verachem.com)

See structural alignment software for structural alignment of proteins. (wikipedia.org)
Conclusions The SVM-Freescore technique is been shown to be a good sequence-based analysis device for useful and structural characterization of conotoxin protein. (columbiagypsy.net)
TBM method predicts the structure of query protein by modifying the structural framework of its homologous protein with known structure in accordance with template-query alignment. (biomedcentral.com)
Nearly all proteins have structural similarities with other proteins, and in some of these cases, share a common evolutionary origin. (berkeley.edu)
The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)

Many conserved proteins of the bacterial DNA uptake machineries are similar to components of protein secretion and type IV pilus biogenesis systems and often play a dual role ( Hobbs and Mattick, 1993 ). (elifesciences.org)
Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
Previously undetected bacterial homologues were identified for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. (embl.de)

Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)

Furthermore, the proposed approach provides some insight by assessing the significance of recently introduced protein features and string kernels. (videolectures.net)
Furthermore, we examine the performance of our methodology on the SCOP 1.53 benchmark data-set that simulates remote homology detection and examine the combination of various state-of-the-art string kernels that have recently been proposed. (videolectures.net)
Fast protein homology and fold detection with sparse spatial sample kernels. (uni-trier.de)

The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
Comparison of the nucleotide sequence of the M. fermentans 609 ftsZ gene to other ftsZ genes showed a 98% homology with Mycoplasma fermentans strain K7 and approximately 50% homology with Mycoplasma pulmonis and Mycoplasma genitalium. (bgu.ac.il)
However, a significant overlap of gene signatures between teams was observed for the majority of the proteins considered, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the union of the predictor genes of the three teams for multiple proteins. (ibm.com)

Motivation: Using gene expression to infer changes in protein phosphorylation levels induced in cells by various stimuli is an outstanding problem. (ibm.com)

In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. (embl.de)

The N-terminal domains of secretins consist of copies of stacked rings which form a periplasmic channel that connects to IM-associated proteins, forming a multi-component secretion system. (elifesciences.org)
The type 6 protein secretion system (T6SS) is prevalently utilized by Gram-negative bacteria to compete for resources and space. (preprints.org)

One key element in understanding the molecular machinery of the cell is to understand the meaning, or function, of each protein encoded in the genome. (columbia.edu)
This gene encodes a large protein with an estimated molecular weight of 350 kDa, and can be divided into six Duffy-binding-like domains (DBL 1-6) based on several conserved cysteines. (biomedcentral.com)
To design, researchers used molecular structure and sequence homology to guide selection of amino acid residues for creating new-to-nature enzymes that catalyze the desired chemistry. (energy.gov)
Our data support an evolutionarily conserved function for SNX1 from yeast to mammals and provide functional insight into the molecular mechanisms underlying lipid-mediated protein targeting and tubular-based protein sorting. (nih.gov)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)

Fold combinations in multi-domain proteins. (ncbs.res.in)

Notably, the majority of the secreted proteins identified (over 50%) turned out to be "orphans" (those with no known functional homologs). (cdc.gov)

From NCBI Gene: This gene encodes a receptor that belongs to the protein tyrosine kinase Tie2 family. (nih.gov)
The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. (biomedcentral.com)

The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. (biomedcentral.com)

Scientists at Carnegie Mellon University, USA, introduced PeptideBERT, a language model that is capable of predicting the properties of proteins and peptides solely based. (cbirt.net)
Cyclic peptides represent an emerging class of drugs that combine the advantageous attributes of small molecules with those of antibodies or protein-based therapeutics. (cbirt.net)
Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)

A very successful means of inferring the function of a previously unannotated protein is via sequence similarity with one or more proteins whose functions are already known. (columbia.edu)
Comprehending sequence-structure-function relationships is challenging for proteins with low similarity to existing proteins. (cbirt.net)

Loading: 50 ng per lane of human SARS-CoV-2 Spike S1 recombinant protein. (biosensis.com)
When expressed as a recombinant protein in transfected cells, PV 3A cofractionates with endoplasmic reticulum markers ( 66 ), and its single transient expression can disrupt the secretory apparatus ( 23 ) and decrease major histocompatibility complex (MHC) class I expression ( 22 ). (asm.org)

However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. (biomedcentral.com)
A homology search against the M. tuberculosis database identified nine additional secretory protein homologs that lacked a secretory signal sequence. (cdc.gov)

The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)

Our approach uncovers an evolutionary pathway between two protein folds and provides a methodology to identify secondary structure switching in other protein families. (bvsalud.org)

Biegert, A. and Söding, J. (2009) Sequence context-specic amino acid similarities for homology searching. (mpg.de)

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 alpha granules contain hemostatic proteins such as fibrinogen, vWf, and growth factors (eg, platelet-derived growth factor and transforming growth factors). (medscape.com)

Vorberg, S., Seemayer, S. and Söding, J. (2018) Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. (mpg.de)

In the closed conformation, HEAT/ARM core domains shield the GTPase-activating protein-related domain (GRD) so that Ras binding is sterically inhibited. (nature.com)
The comparison of several polyisoprenol-based glycosylation pathways from the three domains of life shows that most of the implicated proteins belong to a limited number of superfamilies. (biomedcentral.com)
There are 189281 VWA domains in 166516 proteins in SMART's nrdb database. (embl.de)
As a further test of the power of CATHe to detect more remote homologues missed by HMMs derived from CATH domains, we used a dataset consisting of protein domains that had annotations in Pfam, but not in CATH. (bvsalud.org)
We present evidence that through coincidence detection, the BAR and PX domains efficiently target SNX1 to a microdomain of the early endosome defined by high curvature and the presence of 3-phosphoinositides. (nih.gov)
The encoded protein possesses a unique extracellular region that contains two immunoglobulin-like domains, three epidermal growth factor (EGF)-like domains and three fibronectin type III repeats. (nih.gov)

Several methodologies, capable of handling and generating large-scale protein interaction data, have been employed, such as the experimental techniques of yeast two-hybrid and affinity purification coupled with mass spectrometry [ 17 ]. (biomedcentral.com)

The OM-embedded C-terminal secretin domain likely provides an aperture for DNA and protein translocation through the OM, connecting the periplasm to the extracellular environment. (elifesciences.org)
Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. (embl.de)

Results: The best performance which we report on the SCOP PDB-40D benchmark data-set is a 70% accuracy by combining all the available feature groups from global protein characteristics but also including sequence-alignment features. (videolectures.net)
Examples of problems with complex outputs are natural language parsing, sequence alignment in protein homology detection, and markov models for part-of-speech tagging. (cornell.edu)

Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: protein or nucleotide. (wikipedia.org)
Alignment type: local or global *Sequence type: protein or nucleotide *Sequence type: protein or nucleotide Please see List of alignment visualization software. (wikipedia.org)
New and improved alignment approaches are required for such proteins to. (cbirt.net)

A simplified viral RNA extraction method based on magnetic nanoparticles for fast and high-throughput detection of SARS-CoV-2. (cdc.gov)
SARS infection can be mediated by the binding of the viral spike protein, a glycosylated 139 kDa protein and the major surface antigen of the virus, to the angiotensin-converting enzyme 2 (ACE2) on target cells. (biosensis.com)
NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)

Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. (biomedcentral.com)
The intra-species protein phosphorylation challenge organized by the IMPROVER consortium provided the framework to identify the best approaches to address this issue. (ibm.com)
Here, we report a comprehensive secretome (600 proteins) of this species, which was identified using a multipronged strategy based on genetic/genomic, proteomic, and bioinformatic approaches. (cdc.gov)
The revelation of these species-specific orphan proteins offers a hitherto unexplored repertoire of potential targets for diagnostic, therapeutic, and vaccine research in this emerging lung pathogen. (cdc.gov)

The resulting algorithm, when tested on its ability to recognize previously unseen families from the SCOP database, yields significantly better remote protein homology detection than SVM-Fisher, profile HMMs and PSI-BLAST. (columbia.edu)
The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. (biorxiv.org)

The var2CSA gene, which is a member of the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family, may have an important role in PAM disease and immunity. (biomedcentral.com)

In this work, FMDV 3A homodimerization was evidenced by an in situ protein fluorescent ligation assay. (asm.org)

Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)

It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. (biomedcentral.com)
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 poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)

In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. (biomedcentral.com)
Note that not all tags are clearly annotated in the PDB , so we intend to improve our detection algorithm in future stable SCOPe releases. (berkeley.edu)

Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing. (cdc.gov)

A reporter-gene-fusion-based genomic library that was custom-generated in this study enabled the detection of 23 secretory proteins. (cdc.gov)

Protein structure is fundamentally important to understand protein functions. (biomedcentral.com)
The model accuracy of TBM method critically depends on protein features and the scoring functions that integrate these features. (biomedcentral.com)

We have developed a series of novel approaches to protein biophysics based on ideas from information theory and sign. (rochester.edu)

A homology model of the PilQ protein was fitted into the cryo-EM map. (elifesciences.org)
The screenshot of the tool is shown in Fig. 1 which shows six steps required for building a homology model with the help of EasyModeller. (biomedcentral.com)

As a GTPase-activating protein, a key function of Nf1 is repression of the Ras oncogene signalling cascade. (nature.com)
MID1 gene mutations lead to a decrease in midline-1 function, which prevents protein recycling. (medlineplus.gov)
The resulting accumulation of proteins impairs microtubule function, leading to problems with cell division and migration. (medlineplus.gov)

Anatomy2

Organisms5

Chemicals and Drugs26

Analytical, Diagnostic and Therapeutic Techniques and Equipment48

Psychiatry and Psychology1

Phenomena and Processes38

Disciplines and Occupations3

Information Science10

Health Care8

Sequences19

Structures14

Eukaryotic5

Structure prediction7

Probabilistic1

Classification10

Methods8

Computational3

Structural5

Bacterial3

Prediction of protein1

Kernels3

Genes3

Infer1

Willebrand1

Secretion system2

Molecular5

Fold1

Functional1

Kinase2

Classify1

Peptides3

Similarity2

Recombinant protein2

Homologs2

Encodes1

Secondary1

Similarities1

Platelet-derive2

Contact prediction1

Domains6

Experimental1

Extracellular2

Sequence-alignment2

Alignment3

Viral3

Species4

Remote2

Immunity1

Assay1

Virulence1

Predict2

Intracellular Membranes1

Algorithm2

Genome1

Genomic1

Functions2

Approaches to protein1

Model2

Function3