Dwight McGee Jr. For more information about previous contributors, please see History. Table of Contents. Rigid and Flexible Ligand Docking. Pharmacophore Matching Similarity Score. Hungarian Matching Similarity Score.
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DOCK 6. DOCK 6 Tutorial. IC-6 Manual chinese. EDIUS 4. Introduction to DOCK Introduction 1. General Overview 1. Installation 1. DOCK 2. Overview 2. History 2. Command-line Arguments 2.
The Parameter Parser 2. Ligand File Input 2. Orienting the Ligand 2. Sphere Matching 2. Critical Points 2. Chemical Matching 2. Macromolecular Docking 2. Ligand Flexibility 2.
Anchor-and-Grow 2. Identification of Rigid Segments 2. Manual Specification of Non-rotatable Bonds 2. Identification of Flexible Layers 2. Pruning the Conformation Search Tree 2. Internal Energy Calculation 2. Time Requirements 2. Scoring 2. Contact Score 2. Grid-Based Score 2. DOCK 3. Continuous Score 2. Minimization 2. Parameter Files 2. Atom Definition Rules 2. Ligand File Output 2. Accessories 3. Grid 3. Overview 3. Bump Checking 3. Contact Scoring 3. Energy Scoring 3.
Docktools 3. Chemgrid 3. Ligand Desolvation 3. Occupancy Desolvation 3. Grid Conversion 3. Nchemgrids 3. Sphgen 3. Critical Points 3. Chemical Matching 3. Output 3. Showbox 3. Showsphere 3. Sphere Selector 3. Antechamber 3. Amber Score Preparation Scripts 4. Tripos MOL2 Format 4. PDB Format 5. References 6. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known.
A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes. Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket.
Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years.
For more information on past versions of DOCK, click here. With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility.
For more information about the current release of DOCK, click here. Installation DOCK is Unix based scientific software and follows a common installation recipe: download, unpack, configure, build, and test. The simple configuration scheme of DOCK is based on plain text files. Building and testing employ the make command. DOCK installation is so simple and transparent that users have a reasonable chance of correcting problems themselves.
Start with a plain serial installation. Follow the detailed steps 1. The appropriate configuration option is likely gnu; see step 3. Subsequently, additional executables can be installed for parallel, pbsa, etc; see step 6. Here is the quick start for an example gnu parallel installation: cd install;.
If problems occur then read the diagnostics carefully and apply the scientific method. Consult the FAQ. We recommend a full Unix installation. In particular, when you install your emulator, make sure to also install compilers, Unix shells, and perl Devel for Cygwin. All steps below should be performed using Cygwin or another Unix emulator for Windows. When invoked without arguments, print this usage statement and if the configuration file exists then print its creation stamp.
Some configuration files require that environment variables be defined; these requirements are listed in the files and emitted by configure. Note that g77 is still the default Fortran compiler in the gnu config files.
The suite should complete in less than ten minutes; un-passed tests should be examined to determine their significance. The make check command executed from the test directory emits all the differences uncovered during testing; this command is automatically executed by the main make test command above.
The make clean command executed from the test directory removes all files produced during testing; this command is automatically executed by the main make test command above; however, to run tests from a subdirectory of the test directory, one should explicity execute make clean. NOTE: Some failures are not significant. For example, differences in the tails of floating point numbers may not be significant. The sources of such differences are frequently platform dependencies from computer hardware, operating systems, and compilers that impact arithmetic precision and random number generators.
In addition, the reference outputs are from a 32 bit platform, and this can cause false positives on 64 bit platforms; in particular, differing numbers of Orientations or Conformations and different Contact or Grid scores. We are working on increasing the QC suite's resilience to these issues. For now, apply common sense and good judgment to determine the significance of a possible failure.
Note that some number of failures is rarely an indication of real problems, but if almost every test fails then something is amiss. But other MPI implementations can be accommodated probably with the only extra effort of editing the config. One corrective approach is to use manual linking; add to the LIBS definition in config. Version 6. In particular, for AMBER scoring of RNA receptors, the distance movable region can be applied with explicit waters and the preparation can neutralize to a total charge of zero and can solvate with water.
2019 DOCK tutorial 3 with PDBID 3JQZ
DOCK 6. DOCK 6 Tutorial. IC-6 Manual chinese. EDIUS 4. Introduction to DOCK Introduction 1.
DOCK 6: Impact of New Features and Current Docking Performance
DOCK is a molecular docking program used in drug discovery. It was developed by Irwin D. Kuntz, Jr. This program, given a protein binding site and a small molecule, tries to predict the correct binding mode of the small molecule in the binding site, and the associated binding energy. Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads.
DOCK 6.9 Users Manual
Using the object oriented model, it is functionally separated into independent components classes, methods , allowing a high degree of modularity and programming flexibility. Accessory programs are written in a variety of languages including C and Fortran Source code is available for all programs. Some runs may require considerably more disk space and more memory. With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click. Jump to: navigation , search.