Service Search Product Search Gene Search
HOME

SERVICES

• Protein Biotinylation Service • Custom Lysate Preparation Service • Immunogenicity Test Service > Anti-Drug Antibody (ADA) Evaluation Service > Neutralizing Antibody (NAb) Test Service • Anti-Drug Antibody (ADA) Evaluation Service • Neutralizing Antibody (NAb) Test Service • Thanksgiving Day Sale • Enzyme Target & Activator & Inhibitor Screening Service • GPCR Screening Service • Ion Channel Screening Service • Bio-Layer Interferometry (BLI) • Electrophoretic Mobility Shift Assay (EMSA) Service • Transcription Factor Analysis > Electrophoretic Mobility Shift Assay (EMSA) Service > Chromatin Immunoprecipitation (ChIP) Assay Service > DNase I Footprinting Assay Service • Transporter Screening Service • Chromatin Immunoprecipitation (ChIP) Assay Service • Enzyme Activity Assay Service • DNase I Footprinting Assay Service • Co-Immunoprecipitation (Co-IP) • Surface Plasmon Resonance (SPR) Service • Pull Down Assay • Protein Mutant Library Construction • C1 Expression System • Protein Conjugation Service on Beads • Bacteria Expression • Yeast Expression • Mammalian Cell Expression • Insect Cell Expression • Animal-Free Expression • Cell-Free Protein Expression • Large-Scale Protein Production • PEGylation Products and Services > Custom PEGylation Services > PEGylation Products • Basic Protein Characterization • Protein Labeling • Stable Cell Line Construction for Protein Expression • Protein Mutagenesis • Protein Interaction Analysis Services > Bio-Layer Interferometry (BLI) > Co-Immunoprecipitation (Co-IP) > Surface Plasmon Resonance (SPR) Service > Pull Down Assay > Yeast Two-Hybrid Screening > Membrane-Based Yeast Two-Hybrid Screening > CLIP-Seq Service > Protein Binding Site Mapping > Isothermal Titration Calorimetry > Membrane Protein Binding Screening and Profiling • Yeast Two-Hybrid Screening • Membrane-Based Yeast Two-Hybrid Screening • Recombinant Protein or Antibody Production • Protein Expression Systems > Nicotiana Tabacum Expression System > Bacterial Expression Systems(E. coli / Bacillus) > Yeast Expression Systems(P pastoris / S cerevisiae) > Baculovirus-insect Cell Expression Systems > Mammalian Expression Systems(CHO / 293) • PEGylation Services • Stable Cell Line Construction for Protein Expression • Process Development • cGMP Manufacturing • QC and QA • Bacterial Manufacturing • CLIP-Seq Service • Protein Binding Site Mapping • Quantum Dot Labeling • Protein Expression > Custom Lysate Preparation Service > C1 Expression System > Protein Co-Expression Service in E. coli System > Protein Co-Expression Service in Mammalian Cells > Trimeric Protein Production Service > Lettuce Transient Expression System > Baculovirus-Mammalian cell Protein Expression System > Fusion protein expression • Protein Co-Expression Service in E. coli System • Protein Co-Expression Service in Mammalian Cells • NovEgg Expression System • ADME/Tox Prediction • Pharmacophore Modeling • Screening and Profiling Services > Enzyme Target & Activator & Inhibitor Screening Service > GPCR Screening Service > Ion Channel Screening Service > Transporter Screening Service • Trimeric Protein Production Service • Incorporation of Bioorthogonal Handles > Incorporation of Unnatural Amino Acids > Incorporation of Unnatural Sugars > Direct Chemical Modification • Incorporation of Unnatural Amino Acids • Incorporation of Unnatural Sugars • Protein/Peptide Crosslinking > Enzymatic Crosslinking Services > Photocrosslinking Services > Chemical Crosslinking Services • Enzymatic Crosslinking Services • Photocrosslinking Services • Chemical Crosslinking Services • Direct Chemical Modification • Protein-Fluorophore Bioconjugation • Custom PEGylation Services • PEGylation Products • Target Protein Degradation - Proteolysis Targeted Chimera (PROTAC) • Induced Protein Degradation > Target Protein Degradation - Proteolysis Targeted Chimera (PROTAC) > Hydrophobic Tag Services > Destabilization Domains (DDs) • Hydrophobic Tag Services • Destabilization Domains (DDs) • Drug Development • Protein Analysis > Cell-based Kinase Assays > Protein Aggregation Analysis > Complement Component Assays > Functional Complement Assays • Protein Production > Anaerobic Fermentation > Cell Medium Development and QC Tests • Anaerobic Fermentation > Lactic Acid Bacteria Fermentation • Cell-based Kinase Assays • Isothermal Titration Calorimetry • Lactic Acid Bacteria Fermentation • Protein Aggregation Analysis Nicotiana Tabacum Expression System • Lettuce Transient Expression System • Membrane Protein Binding Screening and Profiling • Baculovirus-Mammalian cell Protein Expression System • Complement Component Assays • Functional Complement Assays • Fusion protein expression • Cell Medium Development and QC Tests

CONTACT US

Tel: 1-631-448-8149
Fax: 1-631-938-8127

Fold Recognition

Knowledge about the tertiary structure of a protein is critical for understanding of its biological function and for the discovery of novel therapeutics. Computational prediction of protein structure is a powerful alternative and supplementary approach to experimental methods such as X-ray crystallography, NMR and cryo-EM. An important task in protein structure prediction is to identify proteins that have similar tertiary structures, which can be used as a template to model the unknown structure of another protein. The process for identifying these structurally similar proteins and is called fold recognition (or threading), a useful method for predicting the structure of a query protein, especially when the query protein shares a low sequence level identity (i.e. <25%) with other proteins with known structure.

Profacgen provides our expertise in helping recognize the correct structural fold among known template protein structures for a target protein by combining sequence profile-profile alignment with multiple structural information. Our approach starts with the construction of a structure template database/library, and then incrementally replacing the sequence of a known protein structure in a library with a query sequence of unknown structure. Alignment of the target sequence with each of the structure templates is achieved by optimizing the designed scoring function. The process is repeated against all known 3D structures in the template database until an optimal fit is found. The most statistically probable alignment is selected as the threading prediction and a structural model is constructed for the target by placing the backbone atoms of the target sequence at their aligned backbone positions of the selected structural template. Unlike sequence-only comparison, these methods take advantage of the extra information made available by 3D structure information. The resultant structural models are all quality validated and can be used downstream in silico or experimental work such as protein engineering and drug design.

Protein structure prediction by fold recognition (threading)

Protein structure  prediction by fold recognition (threading)

Features

  Accurate sequence and structural alignment algorithms for remote homology identification
  1D-3D profiles for similarity comparison
  Template database construction
  Uses functional domain information and sequential evolution information
  Knowledge based scoring function containing mutation potential, environment fitness potential, pairwise potential, secondary structure compatibilities, gap penalties, etc.
  Multiple threading methods to identify converged solution
  Hybrid methods combining threading with other structure prediction methods
  Validation of structure/sequence match by energy calculation

The output includes information about template proteins, the query-template alignments and most importantly full-length models of the target protein. We can also customize the service according to the specific requirements from our customers and integrate our computational procedures into your workflow. Please do not hesitate to contact us for more details about our fold recognition service.

CONTACT US
Email: info@profacgen.com
Tel: 1-631-448-8149
Fax: 1-631-938-8127
Address: 45-1 Ramsey Road, Shirley, NY 11967, USA