protein ligand database

  • Protein-Ligand Complex - MD Tutorials

    GROMACS Tutorial Protein-Ligand Complex. Justin A. Lemkul, Ph.D. Virginia Tech Department of Biochemistry. This example will guide a new user through the process of setting up a simulation system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand. This tutorial focuses specifically on issues related to dealing with the ...

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  • Binding MOAD - The Mother of All Databases

    Binding MOAD, A high-quality protein-ligand database. Nucleic Acids Research 2008, 36, D674-D678. Carlson Lab (C) 2005 The Regents of the University of Michigan

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  • Protein ligand interaction database (PLID) - ScienceDirect

    A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins.

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  • CREDO: A Protein–Ligand Interaction Database for Drug ...

    1/22/2009· CREDO is a relational database comprising protein–ligand interactions derived from structures in the PDB together with relevant data from other sources, in order to integrate structural biology, genomics and chemistry into one fully functional schema.

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  • Binding MOAD, a high-quality protein–ligand database

    Binding MOAD (Mother of All Databases) is a database of 9836 protein–ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled ...

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  • Protein-Ligand Binding Databases - Science

    Protein crystal structures with biologically relevant ligands: BindingDB: Binding database of measured binding affinities for small, drug-like molecules: BioLiP: Ligand-protein binding database: NBDB: Nucleotide Binding DataBase: PDBbind: PDBbind-CN Database of experimentally measured binding affinity data for biomolecular complexes: PSCDB

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  • KEGG LIGAND Database - Genome

    5/1/2019· KEGG LIGAND is a composite database name for COMPOUND, GLYCAN, REACTION, RCLASS, and ENZYME databases, whose entries are identified by C, G, R, RC, and EC numbers, respectively. Each constituent database has its own entry point as shown below.

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  • Protein ligand interaction database (PLID) - ScienceDirect

    A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins.

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  • Binding Database

    BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 1,881,721 binding data, for 7,548 protein targets and 833,792 small molecules. There are 2291 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% ...

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  • Ligand Expo Home

    1/26/2016· Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small ...

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  • Protein Ligand Database (PLD): additional understanding of ...

    9/22/2003· Abstract. Summary: The Protein Ligand Database (PLD) is a publicly available web-based database that aims to provide further understanding of protein–ligand interactions. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities.

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  • Protein Ligand Database - omicX

    This is a non-redundant data set of ligand-binding proteins developed for the current study. To begin with, all the 485 protein-ligand complexes were downloaded from Protein-Ligand Database [] (v1.3 as on 25/01/06). Redundancy among sequences was first removed by using CD-HIT program from [] with a threshold of 40% sequence identity.

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  • (IUCr) Databases for Protein–Ligand Complexes

    This paper discusses databases for protein–ligand data which are accessible via the World Wide Web. A strong focus is placed on the ReLiBase database system which is a new three-dimensional database for storing and analysing structures of protein–ligand complexes currently deposited in the Brookhaven Protein Data Bank (PDB).

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  • UniProt

    Getting started . Text search Our basic text search allows you to search all the resources available. BLAST Find regions of similarity between your sequences. Sequence alignments Align two or more protein sequences using the Clustal Omega program. Retrieve/ID mapping Batch search with UniProt IDs or convert them to another type of database ID (or vice versa) ...

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  • Database Iridium | Protein-Ligand Structure Database

    There are many reasons why this promise has not been fulfilled. The primary motivation behind Iridium is to address the problem of the protein-ligand structural databases used to develop and validate structure-based design tools, in particular, docking algorithms.

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