Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.

By Manfred Hendlich, Andreas Bergner, J. Günther, Gerhard Klebe. Journal of Molecular Biology, 2003

312 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/26517d4de83481fd658ec5b21f0ed56d756d2c11

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Yang Zhang
2. Jianyi Yang
3. Ambrish Roy
4. Daniel Kuhn
5. Gerhard Klebe
6. Chengxin Zhang
7. Zhenling Peng
8. Dusanka Janezic

In Molecular Biology

1. Jianyi Yang
2. Yang Zhang
3. Ambrish Roy
4. Robin Pearce
5. Chengxin Zhang
6. Vladimir Potapov
7. Richard D. Smith
8. Daniel Kuhn

In Pharmacology

1. Yang Zhang
2. Jianyi Yang
3. Daniel Kuhn
4. Gerhard Klebe
5. Chengxin Zhang

Citations in the corpus

• Binding MOAD, a high-quality protein–ligand database (2007, background): “There are several available, including but not limited to Binding MOAD (1), PDBbind (2), LPDB (3), Relibase (4), BindingDB (5), PDBLig (6), MSDsite (7), eF-Site (8), PDB-Ligand (9), SuperLigands (10), PLD (11), HET-PDB (12), sc-PDB (13), PDBsite (14), Ligand Depot (15), AffinDB (16) and KiBank (17).”
• Virtual ligand screening: strategies, perspectives and limitations (2006, methodology): “The analysis of several thousand crystal structures of ligand–protein complexes using the waterbase module in Relibase [65,66] revealed that, in about two-thirds of all cases, a water molecule is involved in ligand binding, frequently mediating contacts between protein and ligand.”
• SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment (2005, background): “A number of web-based servers, including our own [LPC/CSU (3)], provide information on inter- and intramolecular contacts in proteins [PDBsum (4,5), GRASS (6), Relibase (7), RankViaContact (8), STING CONTACTS (9) and Monster (10)].”
• AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB (2005, methodology): “To obtain these data, a helperapplication was generated with a Python-based Relibase toolkit and the data were retrieved from Relibase+ (14,15).”
• BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions (2012, background): “There are some other databases related to the current study, such as Relibase (10) (http://relibase.rutgers.edu) for ligand– protein interactions, Pocketome (11) (http://pocketome. org/) for druggable binding sites, ProtChemSI (12) (http://pcidb.russelllab.org/) for the network of protein– chemical ”
• A new method to detect related function among proteins independent of sequence and fold homology. (2002, methodology): “The definition of a " ligand " thereby obeys the rules set in Relibase.”