What is Plip used for?
The PLIP web service allows for comprehensive detection and visualization of protein–ligand interaction patterns from 3D structures, either directly from the PDB or in user-provided 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?
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995 Feb;8(2):127-34. doi: 10.1093/protein/8.2. 127.
Why are protein-ligand interactions important?
Protein–ligand interactions are fundamental to almost all processes occuring in living organisms. Ligand-mediated signal transmission via molecular complementarity is essential to all life processes; these chemical interactions comprise biological recognition at the molecular level.19-Apr-2010
Why is ligand binding important?
Ligand binding to the C-terminal ligand binding domain is an important regulatory event in AR function, resulting in a conformational change that disrupts an intramolecular interaction between the amino terminus and the carboxy terminus, initiates posttranslational modifications, dissociates the AR from heat shock ...
What is LIGPLOT analysis?
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.
How do you run a LIGPLOT on a Mac?
1b. Linux and macGo to the LigPlus directory where you installed the program. You will see a subdirectory called lib.Go into the lib subdirectory.Among the directories there, you will see two called. exe_mac. ... Go into each of these executable directories in turn and try running the ligplot executable by: ./ligplot.
What is LIGPLOT plus?
Groups Thornton Software > Ligplot+ LigPlot+ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.13-Jul-2012
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 Ethernet cable?
Ethernet may also be used as a direct computer-to-computer communications method using an Ethernet crossover cable . Other point-to-point connections, such as USB host-to-host bridges or cables are also used to transfer files between two computers where a network is not necessary or available.
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, ...
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 .
PLIP
PLIP (Protein-Ligand Interaction Profiler) 是一个蛋白配体非共价相互作用的分析工具；可以分析蛋白配体复合物在原子水平的非共价相互作用，包括氢键，水桥，盐桥，卤键，疏水相互作用，π-堆叠，π-离子相互作用和金属复合物；检测机制主要是基于原子间的空间位置和几何关系。
Others
若要对分子对接的结果进行高通量处理和分析：首先不论是AutoDock4还是vina等等，都可以通过python脚本解析拼接处理得到多个复合物pdb文件，然后利用python调用PLIP自动化对每一个复合物文件进行分析，再用python处理xml文件提取非共价相互作用的数据并处理分析，最后就可以较为方便地得到相互作用数量随氨基酸序列或者配体原子的变化、平均键长键角等信息。