The PLIP server (Salentin et al. 2015) was used to identify non-covalent interactions between proteins and ligand. The Pymol program was used for the visual inspection of the docking poses and to render the 3D molecular images (Delano 2002)....
Full Answer
What can PLIP do for You?
PLIP is complementary to other state-of-the-art web tools such as SwissDock ( 6 ), GalaxySite ( 7) or ProBiS ( 8) and can thus be applied in evaluation of docking results (Figure 4 ), drug design (Figure 5 ), binding site similarity assessment ( 3, 9) and drug repositioning ( 10 ).
What is pypiserver on Zulip?
Chat with us on Zulip! pypiserver is a minimal PyPI compatible server for pip or easy_install . It is based on bottle and serves packages from regular directories. Wheels, bdists, eggs and accompanying PGP-signatures can be uploaded either with pip, setuptools, twine, pypi-uploader, or simply copied with scp.
How do I configure pypiserver?
The main entry-point for configuring pypiserver is the pypiserver:app () function. This function returns the internal WSGI-app that you my then send to any WSGI-server you like.
What is Plip used for?
PLIP is the first web service to provide comprehensive analysis and visualization of non-covalent protein–ligand interactions with one-click loading of structures.
What is protein-ligand interaction?
Interactions. The protein-ligand complex is a reversible non-covalent interaction between two biological (macro)molecules. In non-covalent interactions there is no sharing of electrons like in covalent interactions or bonds.
How do you cite a Ligplot?
Wallace A C, Laskowski R A & Thornton J M (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Prot.
What is ligand in bioinformatics?
Ligand or guest or key. The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer. Docking. Computational simulation of a candidate ligand binding to a receptor.
How does a ligand work?
A ligand is a molecule that binds another specific molecule, in some cases, delivering a signal in the process. Ligands can thus be thought of as signaling molecules. Ligands interact with proteins in target cells, which are cells that are affected by chemical signals; these proteins are also called receptors.
What is LIGPLOT used for?
In bioinformatics, LIGPLOT is a computer program that generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. The LIGPLOT is used to generate images for the PDBsum resource that summarises molecular structure.
Is LIGPLOT a free software?
Available free. To receive a licenced version of the programs, please go to: Academic licence.
What is molecular docking studies?
Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct. Depending upon binding properties of ligand and target, it predicts the three-dimensional structure of any complex.
What is a PLIP port?
The Parallel Line Internet Protocol ( PLIP) is a computer networking protocol for direct computer-to-computer communications using the parallel port normally used for connections to a printer . The Parallel Line Internet Protocol provides Link Layer services for the Internet Protocol, the protocol used for forming small local area networks ...
What is SLIP cable?
An analogous feature for serial communications ports is the Serial Line Internet Protocol (SLIP), using null-modem cables, but allows transfer of four bits at a time rather than one. It generally works at higher bitrates. The method is based on the "Crynwr" standard devised by Russ Nelson .
What is Internet Protocol Suite?
The Internet Protocol Suite is the standards-based networking model and software specification for forming small and large computer networks, from local area networks to global communication systems, such as the Internet. It is usually implemented by software and hardware features that use Ethernet network interface cards, cabling, ...
Abstract
With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing.
MOTIVATION
The Protein Data Bank (PDB) ( 1) is continuously growing and recent advances in structure prediction and experimental methods such as cryoEM will further accelerate this growth. The vast majority of protein structures in PDB contain ligands and therefore it is important to understand how these ligands interact with their targets.
PLIP WEB SERVER AND COMMAND-LINE
The PLIP web server provides an easy-to-use interface (Figure 1 ), which takes as input either a PDB ID or a custom structure in PDB format (e.g. result files from docking or molecular dynamics software).
PLIP FOR DNA AND RNA
PLIP’s main focus so far was the detection of interactions between small molecules and proteins. However, with the constant growth of nucleic acid structure data, a large proportion of over 7% of the PDB (12460 structures) contains DNA and RNA (Figure 2 ).
PLIP AND OTHER TOOLS
There are a number of tools ( 29–37) analysing ligand–target interactions, but apart from one, they have a different focus and therefore suffer from some limitations: ( 29–33) detect only a limited set of interaction types and do not offer 3D visualisation, ( 34) requires extensive preparation of input files, ( 38) is only commercially available and ( 35, 36) are limited to binary interaction fingerprints and do not cover DNA and RNA.
CONCLUSION
Interactions between nucleic acids and small molecules play a crucial role in various biological processes and have a strong impact on drug discovery.
ACKNOWLEDGEMENTS
The authors would like to thank Sven Schreiber, Alexandre Mestiashvili and Christoph Leberecht for their technical support and valuable feedback.
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA
There it is: An update on the PLIP NAR Nucleic Acids Research paper together with a fresh version of the PLIP web server. PLIP is probably the most […]
PharmAI Now Official Maintainer of PLIP
PharmAI takes over the maintenance of the Protein-Ligand Interaction Profiler (PLIP). PLIP, a command line tool and a web service for fully automated characterization of non-covalent […]
Abstract
The characterization of interactions in protein–ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community.
INTRODUCTION
The Protein Data Bank (PDB) ( 1) hosts nearly 100 000 deposited protein structures, with over 75% of them solved in complex with a small molecule ligand. Binding of a ligand to its host protein requires a specific arrangement of attractive, typically non-covalent contacts between both molecules.
WEB SERVER DESCRIPTION
PLIP focuses on one-click processing of protein structures for the detection of interaction patterns. There are other tools, web pages and databases ( 11–20) as well as software from Chemical Computing Group (MOE), Accelrys and CLC bio available. Many of those tools, however, are commercial or can be used for visualization purposes only.
COMMAND-LINE TOOL DESCRIPTION
The python source code of PLIP is available as open-source software and allows to run computations locally. Additional to the features of the web server, the PLIP command-line tool offers advanced settings for output files and thresholds.
PLIP ALGORITHM
PLIP uses four steps to detect and report relevant interactions: structure preparation, functional characterization, rule-based matching and filtering of interactions (Figure 3A–D ). The analysis is exemplified by Bacillus subtilis DegV protein binding palmitic acid (PDB ID 3FYS).
VALIDATION
With the initial release of PLIP, we have included a test suite with 30 literature-validated examples (see Supplementary Data). They comprise diverse cases of protein–ligand complexes from PDB, covering all interaction types detectable by PLIP and resolutions from 1.2 to 3.3 Å.
EXAMPLES
PLIP can be used for both—structures from the PDB archive and structure files from other tools. It is therefore possible to integrate PLIP into pipelines for analyses related to protein–ligand binding, e.g. post processing of docking results or inhibitor design.
What is a PLIP?
PLIP can characterize interactions between ligands and DNA/RNA. A special mode allows to switch from treating DNA/RNA molecules as ligands to treating them as part of the receptor in the structure. If a protein is present, too, interactions of the ligand with both, protein and nucleic acids, will be shown. To use this mode, start PLIP with the option --dnareceptor.
How does PLIP work?
PLIP uses a rule-based system for detection of non-covalent interactions between protein residues and ligands. Information on chemical groups able to participate in a specific interaction (e.g. requirements for hydrogen bond donors) and interaction geometry (e.g. distance and angle thresholds) from literature are used to detect characteristics of non-covalent interactions between contacting atoms of protein and ligands. For each binding site, the algorithm searches first for atoms or atom groups in the protein and ligand which could possibly be partner in specific interactions. In the second step, geometric rules are applied to match groups in protein and ligand forming an interaction.
What is a plip algorithm?
The PLIP algorithm uses a rule-based detection to report non-covalent interaction between proteins and their partners. The current settings are based on literature values and have been refined based on extensive testing with independent cases from mainly crystallography journals, covering a broad range of structure resolutions. For most users, it is not recommended to change the standard settings. However, there may be cases where changing detection thresholds is advisable (e.g. sets with multiple very low resolution structures).
Motivation
The Parallel Line Internet Protocol (PLIP) is a computer networking protocol for direct computer-to-computer communications using the parallel port normally used for connections to a printer.
The Parallel Line Internet Protocol provides link layer services for the Internet Protocol, the protocol used for forming small local area networks and large computer networks, such as the Internet, enabling computers without standard dedicated networking hardware, such as Ethernet, but wit…
Plip Web Server and Command-Line
Plip For DNA and RNA
Plip and Other Tools
Conclusion
Acknowledgements
Funding
- The PLIP web server provides an easy-to-use interface (Figure 1), which takes as input either a PDB ID or a custom structure in PDB format (e.g. result files from docking or molecular dynamics software). Moreover, the advanced options in the input section allow the users to modify the default settings of PLIP according to their special requirements...