Tag: structure prediction


Found 35 sources
Source Match ReputationScore*

SWISS-MODEL Repository of 3D protein structure models


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.
100%

CATH Protein Structure Classification


The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class ( ...
91%

Structural Classification Of Proteins


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 ...
84%

Information system for G protein-coupled receptors (GPCRs)


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. ...
69%

Nucleic Acids Database


The NDB 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 learn about nuclei ...
68%

Group II introns database


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 ...
63%

Molecular Modeling Database (MMDB)


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.
62%

Protein Model Database


The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.
58%

SNPeffect


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 ...
58%

HotRegion


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 ...
58%

ITS2


Predicted structures of internal transcribed spacer 2 (ITS2)
57%

The RNA Modification Database (RNAMDB)


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 ...
56%

MINAS - A Database of Metal Ions in Nucleic AcidS


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 ...
55%

NNDB


Nearest Neighbor parameters for predicting RNA folding
54%

Protein-Chemical Structural Interactions


Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.
53%

RNA Characterization of Secondary Structure Motifs


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 ...
52%

Nucleic Acid Phylogenetic Profile


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 ...
51%

DOMINE


Known and predicted protein domain interactions observed in PDB entries,
50%

PROFEAT


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 ...
49%

SCOR


Database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.
49%

non-B DB


non-B DNA forming motifs in mammalian genomes
47%

MolMovDB


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.
47%

DIMA


Domain interaction map: experimental and predicted protein domain interactions
45%

Protein Geometry Database


Protein conformation and bond angles and lengths
45%

Apo and Holo structures DataBase


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 ...
45%

PCDB


Protein Conformational Diversity database
44%

BSDB


Biomolecule Stretching Database
44%

3DNALandscapes


Conformational features of DNA
44%

SAHG


Structural Atlas of Human Genome
43%

SPRITE


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 ...
42%

Structural Genomics of Histone Tail Recognition


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 ...
40%

HASP


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 ...
40%

Thera-SAbDab


the Therapeutic Structural Antibody Database | The Structural Antibody Database | (Therapeutic Structural Antibody Database) | Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link] | SAbDab paper: Dunbar, J., ...
39%

GSDB


A database of 3D chromosome and genome structures reconstructed from Hi-C data. Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,. GSDB : Genome Structure Database.
38%

DIGIT


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.
37%

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