Protein Sequence Analysis and Function Prediction

Creative BioMart offers comprehensive Protein Sequence Analysis and Function Prediction Services , supporting both experimental and computational research. Leveraging advanced bioinformatics technologies, we classify proteins into families, predict functional domains and important sites, and annotate sequences with structural and functional information. Our integrated approach combines data from multiple protein signature databases to provide a powerful diagnostic tool. In addition, we provide detailed functional predictions, including secondary structure, intrinsically disordered regions, disulphide bridges, inter-residue contacts, transmembrane structures, protein-protein and protein-DNA interactions, subcellular localization, and the effects of amino acid changes. This service enhances research accuracy and accelerates discovery.

Background and Importance

Understanding protein sequences and predicting their functions are fundamental to modern biology, biotechnology, and therapeutic development. Protein sequence analysis allows researchers to identify evolutionary relationships, classify proteins into families, and predict structural and functional domains. Functional annotation, including enzymatic activity, post-translational modifications, and interaction sites, provides critical insights into protein roles in cellular processes. Accurate predictions support experimental design, drug discovery, and biomarker identification. Creative BioMart has a decade-long history of providing expert bioinformatics consultations, ensuring that our analyses remain current, reliable, and aligned with the latest genome and proteome data.

Figure 1. Three-dimensional rendering of X-ray diffraction data obtained from over 15 000 single nanocrystal diffraction snapshots recorded at the LCLS.

Protein Sequence Analysis and Function Prediction Services

Creative BioMart provides a comprehensive suite of protein sequence analysis and function prediction services:

Service	Details
Sequence Analysis	Sequence identity, similarity, and homology assessment Protein family classification Domain and motif prediction Identification of key functional sites
Function Prediction	Secondary structure and intrinsically disordered region prediction Disulphide bridge and inter-residue contact mapping Transmembrane beta-barrel structure prediction Subcellular localization annotation Protein-protein and protein-DNA interaction site prediction Enzymatic activity and amino acid change effect prediction
Manual Annotation	Updating Chordata-specific and widely conserved proteins Resolving discrepancies with genome-predicted sequences Revisiting dubious isoforms and sequences derived from experimental artifacts
Continuous Updates	Integration of novel structural, post-translational modification, interaction, and enzymatic activity data Maintenance of up-to-date functional annotations for human and vertebrate proteins

Service Workflow

Key Features

• Accurate sequence alignment and evolutionary analysis
• Integration of multiple protein signature databases
• Detailed functional annotations including structural and interaction information
• Prediction of post-translational modifications, enzymatic activity, and effects of amino acid substitutions
• Manual curation for high-confidence results in human and Chordata-specific proteins
• Continuous updates to maintain relevance with current genome and proteome data

Why Select Our Protein Analysis Expertise

10,000+ Consultations

Proven success in protein sequence analysis

10 + Years

Expertise in protein research and functional prediction

1–2 weeks

Typical turnaround for standard analyses

Multiple Databases

Integrated resources for reliable predictions

Full Function Coverage

From structure to protein interactions

Always Up-to-Date

Continuous revision ensures accuracy

For Every Researcher

Tailored for biologists, computational scientists, clinicians, and students

Manual Annotation Excellence

Specialized in Chordata-specific and widely conserved sequences

Case Studies and Real-World Applications

Case 1: PIRSF family classification system for protein functional and evolutionary analysis

Nikolskaya et al ., 2006. doi:10.1177/117693430600200033

The PIRSF protein classification system is a curated resource designed to reflect evolutionary relationships among full-length proteins and domains. Its primary unit, the homeomorphic family, groups proteins that are both homologous and share full-length sequence similarity with a common domain architecture. Families are classified using integrative sequence and functional analysis, supported by literature review, and summarized in detailed reports with graphical tools for taxonomic distribution, domain architecture, family hierarchy, and phylogenetic trees. By enabling domain- or fold-based searches, PIRSF supports the study of functional convergence, divergence, lineage-specific conservation, and horizontal gene transfer, making it a valuable tool for comparative protein function and evolutionary research.

Figure 2. PIRSF protein family classification and curation workflow. (Nikolskaya et al., 2006)

Case 2: Structure-based protein function prediction using graph convolutional networks

Gligorijević et al., 2021. doi:10.1038/s41467-021-23303-9

The rapid growth of protein sequence databases and the diversity of protein functions present major challenges for automated function prediction. To address this, DeepFRI—a Graph Convolutional Network—predicts protein functions by combining sequence features from a protein language model with structural information. It outperforms existing sequence-based CNNs and scales efficiently to large databases. Incorporating homology models into the training set expands the range of predictable functions, while its de-noising capability ensures robustness even when using predicted structures. Using class activation mapping, DeepFRI enables residue-level, site-specific annotations. Its utility is demonstrated through high-confidence predictions for proteins in the PDB and SWISS-MODEL.

Figure 3. An example of the gradient-weighted class activation map for ‘Ca Ion Binding’ (right) mapped onto the 3D structure of rat α -parvalbumin (PDB ID: 1S3P), chain A (left), annotated with calcium ion binding. The two highest peaks in the grad-CAM activation profile correspond to calcium-binding residues. (Gligorijević et al., 2021)

Client Success Stories in Protein Sequence Analysis and Function Prediction

“Our lab collaborated with Creative BioMart to analyze a panel of novel kinases identified in our oncology screening program. Their team delivered high-quality domain and motif predictions, which allowed us to pinpoint conserved catalytic residues and prioritize candidates for functional assays. The clarity of their annotations saved us weeks of manual curation and significantly streamlined our drug target validation process.”

— Director of Discovery Biology | Mid-Sized Pharmaceutical Company

“We engaged Creative BioMart to predict the structural and functional impact of rare amino acid substitutions found in a patient-derived genetic dataset. Their integrated analysis, including disulphide bridge mapping and enzymatic activity prediction, gave us the confidence to move forward with clinical functional studies.”

— Head of Translational Medicine | Clinical Research Institute

“Our vaccine development group needed comprehensive annotations for viral surface proteins across multiple strains. Creative BioMart combined sequence homology analysis with subcellular localization predictions and protein-protein interaction mapping, providing us with precise insights into potential epitopes. Their analysis was pivotal in designing immunogens with improved cross-strain coverage.”

— Principal Investigator, Vaccine R&D | Global Biotech Company

“For a comparative genomics project, we partnered with Creative BioMart to annotate Chordata-specific proteins across several vertebrate species. Their manual curation resolved discrepancies between predicted genome sequences and experimental isoforms, helping us eliminate erroneous models. The functional predictions, especially regarding intrinsically disordered regions and interaction sites, added valuable depth to our evolutionary study.”

— Senior Bioinformatics Scientist | Academic Research Center

FAQs About Protein Analysis Services

• Q: What makes your protein sequence analysis different from other providers?

  A: Our service integrates multiple leading bioinformatics databases into one powerful platform, ensuring comprehensive and accurate classification of proteins, domain prediction, and functional annotation. Unlike automated-only pipelines, we also provide expert manual curation, particularly for Chordata-specific and conserved proteins, which increases reliability.

• Q: Can you predict the effect of amino acid substitutions on protein function?

  A: Yes. We provide advanced analysis of amino acid changes, including predictions on stability, enzymatic activity, structural alterations, and potential impacts on binding sites. This is especially valuable for studying genetic variants and rare mutations in disease-related research.

• Q: Do you only provide sequence alignment, or also functional insights?

  A: We go beyond simple sequence alignment. Our services include predictions of secondary structure, intrinsically disordered regions, disulphide bridges, subcellular localization, protein-protein interaction sites, protein-DNA binding sites, and transmembrane beta barrel structures. This ensures a full picture of protein behavior.

• Q: How do you handle discrepancies between predicted sequences and experimental data?

  A: We continuously update and verify sequences, revisiting dubious isoforms or artifacts from gene model predictions. By integrating genomic predictions with experimental evidence, we ensure your dataset reflects the most accurate and up-to-date information.

• Q: Who can benefit from your service?

  A: Our services are designed for experimental biologists, computational scientists, clinicians, pharmaceutical researchers, educators, and students alike. Whether you are validating a drug target, annotating a genome, or teaching protein biology, we provide tailored solutions.

• Q: How quickly can I expect results?

  A: Turnaround times vary depending on project complexity, but thanks to our in-house expertise and streamlined workflow, we typically deliver results within a timeframe significantly shorter than most competitors, without compromising accuracy.

References:

1. Nikolskaya AN, Arighi CN, Huang H, Barker WC, Wu CH. PIRSF family classification system for protein functional and evolutionary analysis. Evol Bioinform Online. 2006;2:117693430600200033. doi:10.1177/117693430600200033
2. Gligorijević V, Renfrew PD, Kosciolek T, et al. Structure-based protein function prediction using graph convolutional networks. Nat Commun. 2021;12(1):3168. doi:10.1038/s41467-021-23303-9