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Protocols

BioLiP specifications

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Unique identifier OMICS_03006
Name BioLiP
Restrictions to use None
Maintained Yes

Publication for BioLiP

BioLiP citations

 (17)
library_books

Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology

2018
Cell Rep
PMCID: 5873459
PMID: 29562182
DOI: 10.1016/j.celrep.2018.02.085

[…] ning sequences were classified as monomers. Heteromer PDB structures were defined as structures with chains from minimum two different proteins, irrespectively of the length of the chains.We used the BioLiP database () of protein-ligand interactions to determine ligand binding residues and whether a ligand is bound to several protein chains or a single one. BioLiP is a semi-manually curated databa […]

call_split

The Immunological Regulation Roles of Porcine β 1, 4 Galactosyltransferase V (B4GALT5) in PRRSV Infection

2018
PMCID: 5837993
PMID: 29546034
DOI: 10.3389/fcimb.2018.00048
call_split See protocol

[…] a Bank (PDB) through the multi-threaded method LOMETS, which built a full-length atomic model through iterative template fragment simulated atomic assembly. The 3D model was then threaded through the BioLiP for ligand-protein binding database to insight into the function of the target protein. Subsequently, I mapped its critical domains using PyMOL software (https://pymol.org/2/). Amino acid seque […]

library_books

In silico structural and functional prediction of African swine fever virus protein B263R reveals features of a TATA binding protein

2018
PeerJ
PMCID: 5825884
PMID: 29492339
DOI: 10.7717/peerj.4396

[…] h.edu/COACH/) bundled TM-site based on existing benchmarked studies was used to compare the structure of a sub-sequence from the first to last binding residues of the queried 3D structure against the Biolip database () (http://zhanglab.ccmb.med.umich.edu/BioLiP/database) to identify potential ligand-binding site residues in the predicted pB263R model 1a structure. Sequence-based pocket and ligand […]

call_split

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns

2017
Sci Rep
PMCID: 5595859
PMID: 28900272
DOI: 10.1038/s41598-017-11924-4
call_split See protocol

[…] re downloaded from the Protein Data Bank (PDB) FTP Archive on Apr 2015. Each structure was analysed with PLIP v1.1.1 using standard settings, resulting in 408,877 complexes. These were filtered using BioLiP, a database for discrimination between biologically relevant ligand and artifacts, to keep 170,219 complexes.To construct BVDU interaction patterns, the PDB structures 2W0S, 2JAW, 1OSN, 2VQS, 1 […]

library_books

Biophysical characterisation of the novel zinc binding property in Suppressor of Fused

2017
Sci Rep
PMCID: 5593987
PMID: 28894158
DOI: 10.1038/s41598-017-11203-2

[…] (30049 HXH hits vs. 202957 AXA hits in human sequences where X is any aminoacid, H is histidine and A is alanine). Amongst those, it is difficult to know how many bind zinc. However, a survey of the BioLiP database (http://zhanglab.ccmb.med.umich.edu/BioLiP) for proteins binding one Zn2+, revealed 311 unique PDB entries with an HXH sequence of the total 9422 zinc binding structures in the PDB. Th […]

library_books

3D QSAR and Molecular Docking Studies on the TcPMCA1 Mediated Detoxification of Scopoletin and Coumarin Derivatives

2017
Int J Mol Sci
PMCID: 5535873
PMID: 28653986
DOI: 10.3390/ijms18071380

[…] mations refined by full-atomic simulations using FG-MD [] and ModRefiner []. Finally, the biological functions of the target proteins were derived by matching the I-TASSER models with proteins in the BioLiP library [,,].Based on identity with the primary sequence of the target TcPMCA1, the crystal structure of the phosphoenzyme intermediate of the rabbit SERCA Ca2+-ATPase (PDB ID code: 3BA6) was r […]


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BioLiP institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

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