Tag: protein structural motifs and surfaces

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical c ...

The international glycan structure repository for glycans published in the literature. Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered and have an accession number assigned as ...

Database of interaction Hotspots across the proteome. Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Ho ...

This is a database of comparative protein structure models of the MIP (Major Intrinsic Protein) family of proteins. The MIPs have been identified from the completed genome sequence of organisms available at NCBI.

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric interna ...

Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for pept ...

ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the ty ...

Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.

Protein-RNA Interface Database

Protein Common Interface Database

Natural and artificial sweetening agents

Protein conformation and bond angles and lengths

The TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins. TMPad includes geometric descriptors of helix ...

fPOP (footprinting Pockets Of Proteins) is a database of the protein functional surfaces identified by shape analysis. In this relational database, we collected the spatial patterns of protein binding sites including both holo and apo forms from more ...

Linear motifs in alpha-helical transmembrane proteins

Biomolecule Stretching Database

Conformational features of DNA

SPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoret ...

An expanded database and web-based tool for structural analysis of DNA-protein complexes. A Database and Web Tool for Structural Analysis of DNA-Protein Complexes. DNAproDB automatically lays out nucleotide and residue interactions maps elegantly. ...

Protein Topology Graph library: Secondary structure-based protein topologies

The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of i ...

Database of proteins classified by their functional surfaces.

Database of Dna REgulatory Motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples.

Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database als ...

The Ligand-Gated Ion Channel database provides access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamat ...

A database of RNA multiloops.

An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.

Surface Plasmon Resonance Database (SPRD) is a surface plasmon resonance database of common factors for better experimental planning.

A3D Database is a database for structure-based protein aggregation predictions for the human proteome

An online tool for designing highly efficient sgRNAs targeting cell surface proteins