SWISS-MODEL homology models mapping to UniProtKB Proteome UP000001816 (Caulobacter crescentus)

PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs. PROSITE is based at the Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland.

A database of proteins identified by various 2-D PAGE and SDS-PAGE reference maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Using the database, users can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot.

SWISS-MODEL homology models mapping to UniProtKB Proteome UP000001584 (Mycobacterium tuberculosis)

SWISS-MODEL homology models mapping to UniProtKB Proteome UP000005640 (Homo sapiens)

A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries.

BASILIScan search with human CDC7 kinase (Uniprot ID: O00311) against all vertebrate sequences available from UniprotKB (both Swissprot and TrEMBL). (CSV 263 kb)

SFLD (Structure-Function Linkage Database) is a hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities.

NCBIfam is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation, which provides a tool for identifying functionally related proteins based on sequence homology. NCBIfam is maintained at the National Center for Biotechnology Information (Bethesda, MD). NCBIfam includes models from TIGRFAMs, another database of protein families developed at The Institute for Genomic Research, then at the J. Craig Venter Institute (Rockville, MD, US).

Protein structure quality information as given by the SWISS-MODEL structure assessment tool.

IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.

HAMAP stands for High-quality Automated and Manual Annotation of Proteins. HAMAP profiles are manually created by expert curators. They identify proteins that are part of well-conserved protein families or subfamilies. HAMAP is based at the SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

Similarity sets created for every amino acid pair to complement semi-conserved amino acid positions with other highly similar amino acids.

IntroductionHomology modeling is a widely used computational technique for predicting the three-dimensional (3D) structures of proteins based on known templates,evolutionary relationships to provide structural insights critical for understanding protein function, interactions, and potential therapeutic targets. However, existing tools often require significant expertise and computational resources, presenting a barrier for many researchers.MethodsProstruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. Integrating Biopython for sequence alignment, BLAST for template identification, and ProMod3 for structure generation, Prostruc streamlines complex workflows into a user-friendly interface. The tool enables researchers to input protein sequences, identify homologous templates from databases such as the Protein Data Bank (PDB), and generate high-quality 3D structures with minimal computational expertise. Prostruc implements a two-stage vSquarealidation process: first, it uses TM-align for structural comparison, assessing Root Mean Deviations (RMSD) and TM scores against reference models. Second, it evaluates model quality via QMEANDisCo to ensure high accuracy.ResultsThe top five models are selected based on these metrics and provided to the user. Prostruc stands out by offering scalability, flexibility, and ease of use. It is accessible via a cloud-based web interface or as a Python package for local use, ensuring adaptability across research environments. Benchmarking against existing tools like SWISS-MODEL,I-TASSER and Phyre2 demonstrates Prostruc's competitive performance in terms of structural accuracy and job runtime, while its open-source nature encourages community-driven innovation.DiscussionProstruc is positioned as a significant advancement in homology modeling, making high-quality protein structure prediction more accessible to the scientific community.

Evaluation results for BrEPS 1.0 and BrEPS 2.0 using UniProt release 2014_10.

This data collection accompanies the manuscript Classifying protein kinase conformations with machine learning.

It is created using thekinactivev0.1tool written in pure Python v3.10. Note that the data areprovided for the reference and reproducibility purposes and will not be compatible with later versions ofkinactive built uponlXtractor 0.1.1. Refer to thekinactive documentationfor instructions on how to obtain an actualized version of the structural kinome collection.

File descriptions:

db_v3.tar.gz -- a structural kinome collection archive. One can unpack it and inspect the contents orload it into the Python interpreter using `kinactive` or `lXtractor` tools.
db_af2.tar.gz -- an AlphaFold2 kinome collection for Swiss-Prot sequences.
default_*_vs.tsv -- structure/sequence variables calculated with lXtractor and used in an interpretable ML pipeline.
*_features.tsv -- lists of ranked features selected by the eBoruta tool for each classifier.
Supplement_labels.tsv -- ML model predictions for each PK domain structure found in db_v3.
predictions_af2.csv -- Active/Inactive and DFG labels predicted for domains in db_af2.

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. SMART is based at EMBL, Heidelberg, Germany.

SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent the entire SCOP superfamily that the domain belongs to. SUPERFAMILY is based at the University of Bristol, UK.

Data used to generate Fig. 4. Summary of the BASILIScan search with all human protein sequences available from UniprotKB/Swissprot against the UniprotKB/Swissprot repository. (CSV 1418 kb)

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types.