Tag: structure prediction

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.

The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is know ...

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. ...

The Nucleic Acids Database contains information about experimentally-determined nucleic acids and complex assemblies. NDB can be used to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.

SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds pe ...

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 ...

Predicted structures of internal transcribed spacer 2 (ITS2)

The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry pro ...

MINAS contains the exact geometric information on the first and second-shell coordinating ligands of every metal ion present in nucleic acid structures that are deposited in the PDB and NDB. Containing also the sequence information of the binding poc ...

Nearest Neighbor parameters for predicting RNA folding

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

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 ...

NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can b ...

The Therapeutic Structural Antibody Database tracks all antibody- and nanobody-related therapeutics recognized by the World Health Organisation (WHO), and identifies any corresponding structures in the Structural Antibody Database (SAbDab) with near- ...

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 ...

Known and predicted protein domain interactions observed in PDB entries,

Database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.

non-B DNA forming motifs in mammalian genomes

The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.

Domain interaction map: experimental and predicted protein domain interactions

Protein conformation and bond angles and lengths

AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo s ...

Protein Conformational Diversity database

Biomolecule Stretching Database

Conformational features of DNA

Experimentally validated Cell Penetrating Peptides

Structural Atlas of Human Genome

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 ...

DescribePROT is a database containing annotations of 13 putative structural and functional properties at the amino acid level for ~1.4 million proteins from 83 popular/model organism, to be extended to hundreds of additional organisms. Users can sear ...

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 ...

A database of 3D chromosome and genome structures reconstructed from Hi-C data. Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,. GSDB : Genome Structure Database.

Server designed as a scientific tool for researchers to visualize their phylogenetic, biochemical, and immunological HA data in the three-dimensional context of the HA structure, in the hopes that the context may help researchers better interpret the ...

An intuitive database of RNA pocket topology information with RNA-ligand data resources.

DbStRiPs (Database of structural repeats in proteins) is a structural repeat database which classifies a protein structure into a structural repeat family based on graph based structural repeat identification algorithm, PRIGSA2.

DIGIT is a database of immunoglobulin variable domain sequences annotated with the type of antigen, the germline sequences and pairing information between light and heavy chains.

Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.

A database of RNA multiloops.

RNA aptamer 3D-structural modeling database.

A repository of cleaned PDB-derived RNA 3D structures.

A database of potential ligand binding sites in the human proteome.

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.

FADB-China is a molecular-level food adulteration database in China based on molecular fingerprints and similarity algorithms prediction expansion.

Dr AFC is a tool for drug repositioning through anti-fibrosis characteristic.

A database that collects tetrads, quadruplexes, and G4-helices found in PDB-deposited structures of nucleic acids. It stores their sequences, secondary and tertiary structures, and motif-specific description including planarity, rise and twist parame ...