Tag: molecular modelling

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 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 euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.

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.

Families of nuclear hormone receptors

Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a c ...

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB ...

ioChem-BD is a digital repository of Computational Chemistry and Materials results. A set of modules and tools aimed to manage large volumes of quantum chemistry results from a wide variety of broadly used simulation packages.

Natural and artificial sweetening agents

In silico drug docking against SARS-CoV2 targets

Structural Atlas of Human Genome

The Biological Structure Model Archive (BSM-Arc) aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce ...

Covalent Inhibitor DataBase

This tool is for understanding the coronavirus proteome and evaluating possible drug targets.

An Unbiased Data Set for Machine Learning and Virtual Screening. 15 target sets, 9780 actives,and 407839 inactives from high-confidence PubChem Bioassay data. LIT-PCBA: A dataset for virtual screening and machine learninig.

Disco Cross Docking Benchmark server for automated pose and ranking prediction of ligand binding.

G-quadruplex Ligands Database

a database for protein-peptide identification based on a hybrid clustering algorithm. PROPEDIA is a database of peptide-protein complexes clusterized in three methodologies: (i) peptide sequences; (ii) structure interface; and (iii) binding sites. P ...

A web application for new bioactive peptides from food protein

The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. FMODB: The database of quantum mechanical data based on the FMO method.

DBCOVP is a database of coronavirus virulent glycoproteins. A Knowledge Based Resource for Exploring the Functional and Immunological Properties of Coronavirus Virulent Glycoproteins for Application in Vaccine Target Discovery.

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 ...

Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. Automatic set up of Molecular Mechanics/Coarse-Grained (MM/CG) simulations for human G Protein-Coupled Receptor (GPCR)/ligand c ...

an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natu ...

CERES is a cryo-EM re-refinement system for continuous improvement of deposited models.

A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design.

DenvInD is a database containing dengue virus inhibitors for clinical and molecular research.

A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.

Toward Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases.

ZINClick is a virtual combinatorial database of over 16 million of 1,4-disubstituted-1,2,3-triazoles (Molecular Weight < 1000), each can be easily synthesized and it is at the same time new and patentable!

Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as ...

A database for improving the rational design of glucose-tolerant β-glucosidases. A database of mutant β-glucosidases. Glutantbase is a database, webtool and method to evaluate mutations for β-glucosidases proteins used in industrial applications. G ...

A database of molecular replacements for ligand design

Sequence conservation profiles of the proteins of known structures

PSnpBind is a large database of protein–ligand complexes covering a wide range of binding pocket mutations and small molecules’ landscape. This database can be used as a source of data for different types of studies, for example, developing machine l ...

Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.

A platform for virtual screening and computer-aided drug designing.

Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring.

A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.

A Database Extension to Visualize Structural Interactome in One-to-many Manner

D3PM is a Comprehensive Database for Protein Motions Ranging from Residue to Domain

CovPDB, a database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank

Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free en ...

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

ConoMode is a database dedicated to collection of the complex 3D structures of conopeptides binding with their target proteins.

KinaFrag is an integrated database to explore the kinase-ligand fragment interaction space. KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery.

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.

GPCR-Sequence-Structure-Feature-Extractor (SSFE). Provides template suggestions and homology models of Class A GPCRs. Identifies key sequence and structural motifs in Class A GPCRs to guide template selection and build homology models.

Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. It is a reliable template-based structure prediction method (PCPCM), and predicted the structures of 180 plant P450s with known functions. In addition, ...