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Use of bioinformatic methods to correlate proteins with biofunctions
Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins
Protein_function_prediction
Type of biological prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its
Protein_structure_prediction
Evaluation of bioinformatic predictors of protein function
of Function Annotation (CAFA) is an ongoing community-driven experiment designed to evaluate computational methods for protein function prediction. Organized
Critical Assessment of Function Annotation
Critical_Assessment_of_Function_Annotation
structure prediction, I-TASSER has a component for structure-based protein function prediction, which provides annotations on ligand binding site, gene ontology
I-TASSER
Biomolecule consisting of chains of amino acid residues
membrane proteins". Genome Biology. 5 (4): 215. doi:10.1186/gb-2004-5-4-215. PMC 395774. PMID 15059248. Sleator RD (2012). "Prediction of Protein Functions".
Protein
Computational analysis of large, complex sets of biological data
segments in proteins. However, protein function prediction can also use external information such as gene (or protein) expression data, protein structure
Bioinformatics
Process in computational biology
biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes
Gene_prediction
Program for solving the travelling salesman problem
use. Concorde has been applied to problems of gene mapping, protein function prediction, vehicle routing, conversion of bitmap images to continuous line
Concorde_TSP_Solver
Protein structure prediction challenge
Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure
CASP
Sternberg's research interests are in protein structure prediction, protein function prediction, prediction of macromolecular docking and interactions
Michael_Sternberg
Polish-Canadian academic (born 1975)
bioinformatics of proteins, with focus on intrinsically disordered proteins, structural genomics, and protein function prediction. His research was funded
Lukasz_Kurgan
Protein without a fixed 3D structure
2008). "First Steps of Protein Structure Prediction" (PDF). In Bujnicki J (ed.). Prediction of Protein Structures, Functions, and Interactions. John
Intrinsically disordered proteins
Intrinsically_disordered_proteins
Three-dimensional arrangement of atoms in an amino acid-chain molecule
often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations
Protein_structure
Predicting 3D protein structure from its sequence
In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its
De novo protein structure prediction
De_novo_protein_structure_prediction
Prediction by observation and computation
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions
Protein–protein interaction prediction
Protein–protein_interaction_prediction
Prediction of where a protein resides in a cell
Protein subcellular localization prediction (or just protein localization prediction) involves the prediction of where a protein resides in a cell, its
Protein subcellular localization prediction
Protein_subcellular_localization_prediction
Artificial intelligence program by DeepMind
developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. It is designed using deep learning techniques. AlphaFold
AlphaFold
Change of a linear protein chain to a 3D structure
structure is essential to function, although some parts of functional proteins may remain unfolded, indicating that protein dynamics are important. Failure
Protein_folding
Species of bacteria
Aloy P, Kalkhof S, et al. (May 2018). "Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori". Mol Cell Proteomics
Helicobacter_pylori
"NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning". Proteins: Structure, Function, and Bioinformatics. 87
List of disorder prediction software
List_of_disorder_prediction_software
Complete set of molecular interactions in a biological cell
molecules (such as those among proteins, also known as protein–protein interactions (PPIs); or between small molecules and proteins.) but can also describe sets
Interactome
Predicted proteins
with other proteins of known functions and annotating possible catalytic site and regulatory site. Structure prediction with biochemical function assessment
Hypothetical_protein
Three dimensional shape of a protein
the prediction of protein structures. Wrinch demonstrated this with the Cyclol model, the first prediction of the structure of a globular protein. Under
Protein_tertiary_structure
Field of molecular biology
a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated
Functional_genomics
Rational design of new protein molecules
understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and
Protein_design
Method used to investigate protein structure
PSI-blast based secondary structure PREDiction (PSIPRED) is a method used to investigate protein structure. It uses artificial neural network machine learning
PSIPRED
Problem in network theory
network, and predicting interactions between genes and proteins in a biological network. Link prediction can also have a temporal aspect, where, given a snapshot
Link_prediction
German computational biology researcher
understanding of evolution, protein structure and protein function. Examples of research carried out in his lab includes the prediction of enzymatic activity
Burkhard_Rost
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization
List of protein subcellular localization prediction tools
List_of_protein_subcellular_localization_prediction_tools
Researcher in AI and Health Technologies
Oron, T. et al. (2013)A large-scale evaluation of computational protein function prediction. Nat Methods 10, 221–227 . https://doi.org/10.1038/nmeth.2340
Karin_Verspoor
Bioengineering process
into the understanding of protein folding and recognition for protein design principles. It has been used to improve the function of many enzymes for industrial
Protein_engineering
Michael; Rhee, Seung Yon (2015). "microProtein Prediction Program (miP3): A Software for Predicting microProteins and Their Target Transcription Factors"
Microprotein
Method of protein structure prediction
structure prediction as it (protein threading) is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank
Threading_(protein_sequence)
entry point to its search function, the latter being a faster iteration. HHpred is an online server for protein structure prediction that uses homology information
HH-suite
Family of proteins which attach to other proteins to modify them
MOdifier) proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function. This
SUMO_protein
Interdisciplinary research area
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of
Molecular_biophysics
Mathematical functions in chemistry
consistently been found to outperform classical scoring functions at binding affinity prediction of diverse protein-ligand complexes. This has also been the case
Scoring_functions_for_docking
Identification and study of genomic sequences
phylogenetic tree visualization software List of protein structure prediction software List of RNA structure prediction software Software section in Sequence analysis
Sequence_analysis
especially for non-homologous proteins (ie. shallow MSA's). Predicted contact maps have been used in the prediction of membrane proteins where helix-helix interactions
Protein_contact_map
Protein engineering technology
Berenberg D, Vatanen T, et al. (May 2021). "Structure-based protein function prediction using graph convolutional networks". Nature Communications. 12
In situ cyclization of proteins
In_situ_cyclization_of_proteins
Academic journal
Proteins: Structure, Function, and Bioinformatics is a monthly peer-reviewed scientific journal published by John Wiley & Sons, which was established
Proteins_(journal)
use protein sequence and/ or protein structure to predict protein aggregation. The table below, shows the main features of software for prediction of protein
Protein aggregation predictors
Protein_aggregation_predictors
has been used in the inference of protein residue contacts, RNA structure prediction, the inference of protein-protein interaction networks, the modeling
Direct_coupling_analysis
Topics referred to by the same term
Assessment of Function Annotation an ongoing community-driven experiment designed to evaluate computational methods for protein function prediction Critics
CAFA
Protein found in humans
Y (July 2017). "COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information". Nucleic Acids
Zinc_finger_protein_226
Software for understanding biological data
algorithms had to be programmed by hand; for problems such as protein structure prediction, this proved difficult. Machine learning techniques such as deep
Machine learning in bioinformatics
Machine_learning_in_bioinformatics
Protein spanning across a biological membrane
transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways
Transmembrane_protein
Protein-coding gene in the species Homo sapiens
spanning base pairs from 118,148,556 to 118,171,011. FAM46C is a protein of unknown function consisting of 391 amino acid residues that are translated from
FAM46C
Ontology database for protein domains
The second concept is to use ontology-labeled protein domains for, for example, protein function prediction. Put it in a simple way, the first concept is
DcGO
Mammalian protein found in Homo sapiens
Y (July 2017). "COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information". Nucleic Acids
C7orf50
Number and arrangement of multiple folded protein subunits in a multi-subunit complex
three levels of protein structure, not all proteins will have a quaternary structure since some proteins function as single units. Protein quaternary structure
Protein_quaternary_structure
Software for protein modeling and analysis
server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure
RaptorX
University in 2018. His research interests include machine learning, protein function prediction and analysis of post-translational modifications. Radivojac received
Predrag_Radivojac
American computer scientist
artificial intelligence. His current research is focused on protein structure and function prediction, 3D genome structure modeling, biological network construction
Jianlin_Cheng
Class of cell surface receptors coupled to G-protein-associated intracellular signaling
understanding how G protein-coupled receptors function". There have been at least seven other Nobel Prizes awarded for some aspect of G protein–mediated signaling
G_protein-coupled_receptor
Protein-coding gene in humans
(April 2010). "I-TASSER: a unified platform for automated protein structure and function prediction". Nature Protocols. 5 (4): 725–38. doi:10.1038/nprot.2010
BEND2
Physical interactions and constructions between multiple proteins
Multiprotein complex Protein domain dynamics Protein flexibility Protein structure Protein–protein interaction prediction Protein–protein interaction screening
Protein–protein_interaction
American computational biologist
application to proteomes for the prediction of protein structure and function, the prediction of small molecule ligand-protein interactions with applications
Jeffrey_Skolnick
American computational biologist
of the microbiome functionality, genetic variant impact and protein function prediction. Her lab develops novel bioinformatics techniques integrating
Yana_Bromberg
properties of characterized nodes. Specifically, they were applied to protein function prediction, cancer gene identification, and discovery of pathways underlying
Graphlets
Biological concepts and questions with insufficient resolutions
proteins used by the team. Accurate prediction of quaternary structure was achieved by AlphaFold3 in 2024. Inverse protein-folding problem (protein design):
List of unsolved problems in biology
List_of_unsolved_problems_in_biology
Protein-coding gene in the species Homo sapiens
"I-TASSER server for protein structure and function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2020-12-14. "PHYRE2 Protein Fold Recognition Server"
C6orf136
to organize information on how proteins are most often classified: by structure, by function, or by location. Proteins may be classified as to their three-dimensional
List_of_proteins
Description of the structure and function of a genome
1093/bioinformatics/btp536. PMC 2773257. PMID 19744993. Vu TT, Jung J (2021). "Protein function prediction with gene ontology: from traditional to deep learning models"
DNA_annotation
Sequence of DNA that determines traits in an organism
for the production of an RNA molecule or a protein that performs some function. The emphasis on function is essential because there are stretches of
Gene
Subsidiary of Alphabet
Proteins: Structure, Function, and Bioinformatics. 88 (8): 1100–1109. doi:10.1002/prot.25892. ISSN 1097-0134. "Groups Analysis: Ligand predictions -
Isomorphic_Labs
and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids
CIROP
Bioinformatics technique
Date, Shailesh V.; Marcotte, Edward M. (2005-05-15). "Protein function prediction using the Protein Link EXplorer (PLEX)". Bioinformatics. 21 (10): 2558–2559
Phylogenetic_profiling
Protein-coding gene in the species Homo sapiens
Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood. C1orf94 gene
C1orf94
Professor of Biochemistry
such as the Critical Assessment of protein Structure Prediction (CASP) and the Critical Assessment of Function Annotation (CAFA). She was elected a
Rita_Casadio
Protein-coding gene in the species Homo sapiens
Y (July 2017). "COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information". Nucleic Acids
SLC46A3
American biochemist and computational biologist (born 1962)
the Rosetta algorithm for ab initio protein structure prediction, which has been extended into a tool for protein design, a distributed computing project
David_Baker_(biochemist)
Bioinformatics software tool
representation of gene and gene product attributes across all species. Protein function prediction Functional genomics Bioinformatics Conesa, A; Götz, S; García-Gómez
Blast2GO
Protein-coding gene in the species Homo sapiens
"Phyre2".[permanent dead link] "I-TASSER Protein Structure & Function Predictions". "PSORT II Prediction". "NCBI Geo Profile". "FAM76A Allen Brain Atlas"
FAM76A
Method of protein structure prediction using other known proteins
Rychlewski, L; Zhang, B; Godzik, A. (1998). "Fold and function predictions for Mycoplasma genitalium proteins". Fold Des. 3 (4): 229–38. doi:10.1016/S1359-0278(98)00034-0
Homology_modeling
Transmembrane protein 151A, also known as TMEM151A, is a protein that is encoded by the TMEM151A gene. The gene encoding transmembrane protein 151A is located
Transmembrane_protein_151A
Tertiary structure prediction tool for protein sequence
and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as fire) are free web-based services for protein structure prediction. Phyre is among
Phyre
Protein-coding gene in the species Homo sapiens
server for protein structure and function prediction". I-TASSER. Yang J, Zhang Y (July 2015). "I-TASSER server: new development for protein structure and
ZNF548
Protein-coding gene in the species Homo sapiens
and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids
IGSF6
American biologist and academic
alternative splicing and nonsense-mediated decay of messenger RNA Protein function prediction using Bayesian phylogenomics In 2010 he was awarded the Overton
Steven_E._Brenner
Self-stable region of a protein's chain that folds independently from the rest
covering protein domains Pfam: database of protein domains Protein Protein structure Protein structure prediction Protein structure prediction software
Protein_domain
Uncharacterized gene
The C3orf38 protein is 329 amino acids in length. A large domain of unknown function, DUF4518, encompasses majority of the C3orf38 protein. This domain
C3orf38
Protein-coding gene in the species Homo sapiens
1093/nar/gkl266. PMC 1538823. PMID 16844986. "I-TASSER server for protein structure and function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2016-05-06. "Motif
LOC105377021
Invention of new medications based on knowledge of a biological target
organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the
Drug_design
cellular proteins are translated and folded in the cytosol with the help of molecular chaperones. Just as proteins must be folded to function in the cytosol
Mitochondrial unfolded protein response
Mitochondrial_unfolded_protein_response
BOINC based volunteer computing project researching protein folding
Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC)
Rosetta@home
Protein–protein interactions in human cells
Rebholz-Schuhmann D (July 2008). "Integrating protein-protein interactions and text mining for protein function prediction". BMC Bioinformatics. 9 (Suppl 8) S2
Human_interactome
Collection of data on conformations of a given protein's amino acid side chains
search times of side-chain packing algorithms used in protein structure prediction and protein design. The first backbone-dependent rotamer library was
Backbone-dependent rotamer library
Backbone-dependent_rotamer_library
3D conformation of a biological sequence, like DNA, RNA, proteins
three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered
Biomolecular_structure
Professor of Bioinformatics
approach to investigate the impacts of disease-causing mutations on protein function. ucl.ac.uk (PhD thesis). University College London. OCLC 1063745930
Christine_Orengo
Computational modeling of molecular interaction
determined experimentally, or can be estimated by a protein structure prediction technique. Protein–nucleic acid interactions feature prominently in the
Macromolecular_docking
Protein-coding gene in the species Homo sapiens
kDa protein in humans that is encoded by the A1BG gene. The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows
Alpha-1-B_glycoprotein
predicting gene and protein functions. Brutlag's lab developed several early databases and algorithms for protein function prediction, including: Emotifs:
Douglas_Lee_Brutlag
Type of artificial neural network
data stream. The logistic map can be used to explore function approximation, time series prediction, and control theory. The map originated from the field
Radial_basis_function_network
Intersection of the fields of evolution and genomics
phylogenomics: Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing
Phylogenomics
Protein-coding gene in the species Homo sapiens
Glutamine-rich protein 2 is a protein that in humans is encoded by the QRICH2 gene on human chromosome 17. The function of QRICH2 protein is mostly unknown
QRICH2
mainly helical proteins, and higher contact order belonging to proteins with a high beta-sheet content. Protein structure prediction methods are more
Contact_order
Type of protein
related protein, thus expanding possible genomic outputs. RBPs function extensively in the regulation of this process. Some binding proteins such as neuronal
RNA-binding_protein
Lattice proteins are highly simplified models of protein-like heteropolymer chains on lattice conformational space which are used to investigate protein folding
Lattice_protein
Protein found in humans
Transmembrane protein 179 is a protein that in humans is encoded by the TMEM179 gene. The function of transmembrane protein 179 is not yet well understood
Transmembrane_protein_179
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
Boy/Male
German, Polish
To Protect
Girl/Female
Hindu, Indian
Fraction of the Cosmos
Girl/Female
Tamil
Rakshita | ரகà¯à®·à®¿à®¤à®¾, ரகà¯à®·à¯€à®¤à®¾Â
Who protect
Rakshita | ரகà¯à®·à®¿à®¤à®¾, ரகà¯à®·à¯€à®¤à®¾Â
Girl/Female
Tamil
Rakshitha | ரகà¯à®·à®¿à®¤à®¾, ரகà¯à®·à¯€à®¤à®¾Â
Who protect
Rakshitha | ரகà¯à®·à®¿à®¤à®¾, ரகà¯à®·à¯€à®¤à®¾Â
Girl/Female
Hindu, Indian
Protect
Girl/Female
Arabic, Australian, Muslim
Protect
Boy/Male
Indian
Friction
Girl/Female
Afghan, Arabic, Australian, Indian, Muslim
Fiction; Romance; Story
Surname or Lastname
English
English : possibly a variant of Porton, a habitational name from Porton in Wiltshire or Poorton in Dorset; both place names are formed with an obscure first element, perhaps the name of a river, + Old English tūn ‘settlement’.Dutch : habitational name for someone from a place named with Dutch poort ‘gate’.
Girl/Female
Hindu
Who protect
Boy/Male
Hindu, Indian
Proven
Boy/Male
Bengali, Indian
Symbol
Boy/Male
Greek Shakespearean
A sea god.
Boy/Male
Hindu
Girl/Female
Afghan, Arabic, Australian, Danish, French, Hebrew, Muslim
Protect
Girl/Female
Bengali, Indian
Fraction of Time
Boy/Male
Buddhist, Indian, Japanese
Mysterious Function
Surname or Lastname
English and French
English and French : regional name from Old French Poitevin, denoting someone from Poitou in western France. The form Potvin has long been established in England and was brought to the U.S. from there. However, French bearers of the surname Poitevin also came to the New World, where their surname underwent a similar transformation on arrival in New England.
Girl/Female
Hindu
Who protect
Boy/Male
Bengali, Indian
Love
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
Boy/Male
American, British, English
Bright; Shining; Place Name; Where Birch Trees Grow
Female
Hindi/Indian
(लीना) Hindi name LINA means "absorbed in; merged." Compare with other forms of Lina.
Girl/Female
Tamil
Anshuka | அநà¯à®·à¯à®•à®¾
Sunbeam, Gentle, Brilliant, Radiant
Boy/Male
Arabic, Indian, Muslim
Protected
Boy/Male
Hindu
Fragrant
Boy/Male
Tamil
Lord Shiva
Girl/Female
American, Australian, British, Christian, Dutch, English, Finnish, French, German, Greek, Latin, Portuguese, Swedish
Maiden
Boy/Male
Hindu, Indian, Kannada, Oriya, Sanskrit, Telugu, Traditional
Felicitous
Biblical
fire of the sun
Girl/Female
Arabic, Muslim
Companion; Bin Umayr Al-hanafi
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
PROTEIN FUNCTION-PREDICTION
a.
Of or related to protein; albuminous; proteid.
n.
The things sold by auction or put up to auction.
n.
The place or point of union, meeting, or junction; specifically, the place where two or more lines of railway meet or cross.
n.
The act of anointing, smearing, or rubbing with an unguent, oil, or ointment, especially for medical purposes, or as a symbol of consecration; as, mercurial unction.
v. t.
To separate by means of, or to subject to, fractional distillation or crystallization; to fractionate; -- frequently used with out; as, to fraction out a certain grade of oil from pretroleum.
a.
Exceedingly variable; readily assuming different shapes or forms; as, an amoeba is a protean animalcule.
a.
Pertaining to the function of an organ or part, or to the functions in general.
n.
A quantity so connected with another quantity, that if any alteration be made in the latter there will be a consequent alteration in the former. Each quantity is said to be a function of the other. Thus, the circumference of a circle is a function of the diameter. If x be a symbol to which different numerical values can be assigned, such expressions as x2, 3x, Log. x, and Sin. x, are all functions of x.
v. i.
To make a solemn declaration (often a written one) expressive of opposition; -- with against; as, he protest against your votes.
n.
The act of feigning, inventing, or imagining; as, by a mere fiction of the mind.
n.
The act of joining, or the state of being joined; union; combination; coalition; as, the junction of two armies or detachments; the junction of paths.
a.
Pertaining to, or connected with, a function or duty; official.
v. t.
To supply with an organ or organs having a special function or functions.
v. t.
To sell by auction.
v. t.
To give sanction to; to ratify; to confirm; to approve.
v. t.
The act of uniting, or the state of being united; junction.
a.
Of or pertaining to Proteus; characteristic of Proteus.
n.
The appropriate action of any special organ or part of an animal or vegetable organism; as, the function of the heart or the limbs; the function of leaves, sap, roots, etc.; life is the sum of the functions of the various organs and parts of the body.
v. t.
To make a solemn declaration or affirmation of; to proclaim; to display; as, to protest one's loyalty.
n.
The act of anointing, or the state of being anointed; unction; specifically (Med.), the rubbing of ointments into the pores of the skin, by which medicinal agents contained in them, such as mercury, iodide of potash, etc., are absorbed.