Commit ac53df75 authored by Jacob Durrant's avatar Jacob Durrant

Updates to docs, replaced CDN urls, etc.

parent fdcf217b
......@@ -8,15 +8,15 @@ WIP
* Fixed a minor bug that sometimes caused malformed example command lines.
* Added links so users can save the receptor/ligand PDBQT input files
generated within the app.
* Created a separate, independent helper app called PDBQTConvert that can
convert files in many other formats (e.g., PDB, XYZ, CAN, SMI) to PDBQT (see
* Created a separate, independent web app called PDBQTConvert that can convert
files in many other formats (e.g., PDB, XYZ, CAN, SMI) to PDBQT (see
`pdbqt_convert/`). This app uses
[openbabel.js](https://github.com/partridgejiang/cheminfo-to-web/)
and is GNU GPL licensed. We distribute it alongside Webina, but as a
separate program.
[openbabel.js](https://github.com/partridgejiang/cheminfo-to-web/) and is
GNU GPL licensed. We distribute it alongside Webina, but as a separate
program.
* Added ways to provide/process input PDBQT files.
* Modified Webina so users can optionally use PDBQTConvert to convert their
input files. Webina communicates with PDBQTConvert at "arms length," via
input files. Webina communicates with PDBQTConvert at "arm's length," via
an iframe.
* Added the ability to draw small-molecule ligands.
* Added a link to optionally remove non-protein residues from the receptor.
......
......@@ -38,13 +38,14 @@ Additional browsers are likely to enable SharedArrayBuffer soon.
## Description of Use ##
### Preparing Receptor/Ligand PDBQT Input Files ###
### Receptor/Ligand PDBQT Input Files ###
As is the case with command-line Vina, Webina accepts input receptor and
ligand files in the PDBQT format. The latest version of the Webina app
interfaces with the PDBQTConvert app (included in the git repository) to
convert these files from other formats (e.g., PDB) to PDBQT. But some advanced
users may wish to provide their own PDBQT files. Such users include:
optionally interfaces with the PDBQTConvert app (included in the git
repository) to convert these files from other formats (e.g., PDB) to PDBQT.
But some advanced users may wish to provide their own PDBQT files. Such users
include:
* Users who wish to have more fine-grained control over the input. For
example, users who wish to specify protonation states, ring-conformational
......@@ -74,7 +75,7 @@ receptor PDBQT files:
Here is an example command: `obabel -xr -ipqr my_receptor.pqr -O
my_receptor.pdbqt`
##### Preparing the Ligand PDBQT File #####
#### Preparing the Ligand PDBQT File ####
We recommend the following steps for those who wish to provide their own
ligand PDBQT files:
......@@ -126,18 +127,33 @@ results. On first visiting the Webina web app, the user encounters the "Input
Parameters" tab. This tab includes several subsections that are useful for
setting up a Webina run.
__Input PDBQT Files.__ The "Input PDBQT Files" subsection allows the user to
__Input PDBQT Files.__ The "Input (PDBQT) Files" subsection allows the user to
select their receptor and ligand files. As is the case with command-line Vina,
these files must be in the PDBQT format. The user can also optionally specify
a known-pose PDB or PDBQT ligand file. This file includes the ligand in its
experimentally determined, correct bound pose (e.g., per X-ray crystallography
or NMR). The known-pose file plays no role in the docking calculation; rather,
it serves as a positive-control reference for evaluating Webina-predicted
ligand poses.
Some users may wish to test Webina without having to provide their own input
files. The optional "Use Example Files" button automatically loads in example
receptor, ligand, and known-pose files.
ligand poses. In our experience, it is often helpful to first benchmark Webina
(or Vina) against a known ligand before using the program to evaluate
compounds with unknown poses and binding affinities.
The "Input (PDBQT) Files" subsection also includes several options to simplify
the process of preparing/testing protein/ligand input files.
* If users wish only to test Webina without having to provide their own files,
they can click the "Use Example Files" button to automatically load example
receptor, ligand, and known-pose files.
* If users specify receptor/ligand input files that are not in the required
PDBQT format, the Webina web app will optionally attempt to convert them to
PDBQT using the PDBQTConvert app. Interactions between the Webina and
PDBQTConvert apps occur at "arm's length" via an iframe.
* If users' receptor files include non-protein residues that might interfere
with docking (e.g., a co-crystallized ligand), they can remove all
non-protein atoms.
* If users do not have a ligand file, they can use a web-based 2D molecular
editor to draw their ligand by hand. PDBQTConvert then converts that 2D
ligand representation to a 3D PDBQT file for docking.
__Docking Box.__ The "Docking Box" subsection allows users to specify the
region of the receptor where Webina should attempt to pose the ligand. This
......@@ -179,7 +195,9 @@ aims to help Vina users who wish to use the Webina web app to setup their
docking boxes and user parameters. A text field provides a mock example of how
to use command-line Vina with the specified parameters. Users can copy this
example, modify it as needed, and paste it into their command-line terminals
to run the desired calculation with the standard Vina executable.
to run the desired calculation with the standard Vina executable. This
subsection also includes links that allow the user to download the
receptor/ligand PDBQT files for command-line use.
__Starting the Webina Calculation.__ Once users click the "Start Webina"
button, the Webina app will switch to the "Running Webina" tab while Webina
......
......@@ -10,7 +10,7 @@
<meta charset="utf-8">
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>Webina</title>
<link rel="shortcut icon" href="favicon.ico"><link href="vendors.0e5b3fc3dceab82cde6c.css" rel="stylesheet"><link href="styles.css.0e5b3fc3dceab82cde6c.css" rel="stylesheet"></head>
<link rel="shortcut icon" href="favicon.ico"><link href="vendors.6bf864e0e87d872d56ba.css" rel="stylesheet"><link href="styles.6bf864e0e87d872d56ba.css" rel="stylesheet"></head>
<body>
<div id="app"></div>
......@@ -24,6 +24,6 @@
<script src="vue.min.js"></script>
<script src="vuex.min.js"></script>
<script src="bootstrap-vue.min.js"></script>
<script type="text/javascript" src="runtime.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="vendors.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="app.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="styles.css.0e5b3fc3dceab82cde6c.js"></script></body>
<script type="text/javascript" src="runtime.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="vendors.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="app.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="styles.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="styles.css.6bf864e0e87d872d56ba.js"></script></body>
</html>
......@@ -110,8 +110,39 @@
<a href="#description-of-use" id="description-of-use" style="color: inherit; text-decoration: none;">
<h2>Description of Use</h2>
</a>
<a href="#preparing-receptorligand-pdbqt-input-files" id="preparing-receptorligand-pdbqt-input-files" style="color: inherit; text-decoration: none;">
<h3>Preparing Receptor/Ligand PDBQT Input Files</h3>
<a href="#pdbqtconvert-web-app" id="pdbqtconvert-web-app" style="color: inherit; text-decoration: none;">
<h3>PDBQTConvert Web App</h3>
</a>
<p>We created the PDBQTConvert web app to better accomodate novice users. Like
Vina, the Webina library accepts receptor/ligand input files only in the PDBQT
format, a PDB-like format that additionally includes atom types and partial
atomic charges. As described in the &quot;Webina and Vina Benchmarks&quot; section
below, a number of command-line and other programs are available for
converting receptor/ligand input files from popular formats (e.g., PDB, SDF,
etc.) to PDBQT. But PDBQTConvert provides an easier way to prepare these files
using a Bootstrap4-powered GUI in the browser. We distribute the PDBQTConvert
app alongside Webina, but as an entirely separate program. Unlike the Webina
library/app codebase, the PDBQTConvert app is GPLv2 licensed, not Apache-2.0.</p>
<p>PDBQTConvert uses the <a href="https://github.com/partridgejiang/cheminfo-to-web/tree/master/OpenBabel/OpenBabel-js">OpenBabel JS
library</a>
to convert receptor and ligand input files from many common formats (i.e.,
CAN, ENT, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PQR, SD, SDF, SMI, SMILES, and
XYZ) to the Webina-compatible PDBQT format. The app can optionally include
branches and torsion trees, as required to indicate which ligand bonds should
be considered rotatable during Webina/Vina docking.</p>
<p>A second option instructs PDBQTConvert to add hydrogen atoms per a
user-specified pH. This feature is particularly useful because PDB receptor
structures derived via X-ray crystallography often lack the resolution
required to place hydrogen atoms, and many popular ligand formats (e.g.,
SMILES strings) do not enumerate explicit hydrogen atoms. And yet Webina/Vina
docking does require that receptor/ligand PDBQT files include polar hydrogen
atoms.</p>
<p>A third option instructs PDBQTConvert to generate 3D coordinates for the input
molecule. Many popular ligand formats (e.g., SMILES strings, flat SDF files,
etc.) do not include 3D atomic coordinates, but Webina/Vina docking requires
fully 3D models.</p>
<a href="#receptorligand-pdbqt-input-files" id="receptorligand-pdbqt-input-files" style="color: inherit; text-decoration: none;">
<h3>Receptor/Ligand PDBQT Input Files</h3>
</a>
<p>As is the case with command-line Vina, Webina accepts input receptor and
ligand files in the PDBQT format. The latest version of the Webina app
......@@ -201,17 +232,33 @@ ligand.pdbqt</code></li>
results. On first visiting the Webina web app, the user encounters the &quot;Input
Parameters&quot; tab. This tab includes several subsections that are useful for
setting up a Webina run.</p>
<p><strong>Input PDBQT Files.</strong> The &quot;Input PDBQT Files&quot; subsection allows the user to
<p><strong>Input PDBQT Files.</strong> The &quot;Input (PDBQT) Files&quot; subsection allows the user to
select their receptor and ligand files. As is the case with command-line Vina,
these files must be in the PDBQT format. The user can also optionally specify
a known-pose PDB or PDBQT ligand file. This file includes the ligand in its
experimentally determined, correct bound pose (e.g., per X-ray crystallography
or NMR). The known-pose file plays no role in the docking calculation; rather,
it serves as a positive-control reference for evaluating Webina-predicted
ligand poses.</p>
<p>Some users may wish to test Webina without having to provide their own input
files. The optional &quot;Use Example Files&quot; button automatically loads in example
receptor, ligand, and known-pose files.</p>
ligand poses. In our experience, it is often helpful to first benchmark Webina
(or Vina) against a known ligand before using the program to evaluate
compounds with unknown poses and binding affinities.</p>
<p>The &quot;Input (PDBQT) Files&quot; subsection also includes several options to simplify
the process of preparing/testing protein/ligand input files.</p>
<ul>
<li>If users wish only to test Webina without having to provide their own files,
they can click the &quot;Use Example Files&quot; button to automatically load example
receptor, ligand, and known-pose files.</li>
<li>If users specify receptor/ligand input files that are not in the required
PDBQT format, the Webina web app will optionally attempt to convert them to
PDBQT using the PDBQTConvert app. Interactions between the Webina and
PDBQTConvert apps occur at &quot;arms length&quot; via an iframe.</li>
<li>If users&#39; receptor files include non-protein residues that might interfere
with docking (e.g., a co-crystallized ligand), they can remove all
non-protein atoms.</li>
<li>If users do not have a ligand file, they can use a web-based 2D molecular
editor to draw their ligand by hand. PDBQTConvert then converts that 2D
ligand representation to a 3D PDBQT file for docking.</li>
</ul>
<p><strong>Docking Box.</strong> The &quot;Docking Box&quot; subsection allows users to specify the
region of the receptor where Webina should attempt to pose the ligand. This
box-shaped volume is typically centered on a known protein pocket or cavity
......@@ -247,7 +294,9 @@ ligand.pdbqt</code></li>
docking boxes and user parameters. A text field provides a mock example of how
to use command-line Vina with the specified parameters. Users can copy this
example, modify it as needed, and paste it into their command-line terminals
to run the desired calculation with the standard Vina executable.</p>
to run the desired calculation with the standard Vina executable. This
subsection also includes links that allow the user to download the
receptor/ligand PDBQT files for command-line use.</p>
<p><strong>Starting the Webina Calculation.</strong> Once users click the &quot;Start Webina&quot;
button, the Webina app will switch to the &quot;Running Webina&quot; tab while Webina
executes. When the calculation is complete, the Webina web app will switch to
......
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......@@ -182,7 +182,7 @@ export function setup(): void {
</span>
</p>
<p>Or click "Convert" below to convert with PDBQTConvert, which should be good enough for most purposes.</p>
<p>Or click "Convert" below to convert with the PDBQTConvert app, which should be good enough for most purposes.</p>
<b-form-checkbox
id="babel-add-hydrogens"
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......@@ -28,35 +28,8 @@
<meta name="description" content="PDBQT Convert" />
<meta name="author" content="Jacob D. Durrant" />
<!-- Latest compiled and minified CSS -->
<link
rel="stylesheet"
href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css"
integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh"
crossorigin="anonymous"
/>
<!-- Optional theme -->
<link
rel="stylesheet"
href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap-theme.min.css"
integrity="sha384-rHyoN1iRsVXV4nD0JutlnGaslCJuC7uwjduW9SVrLvRYooPp2bWYgmgJQIXwl/Sp"
crossorigin="anonymous"
/>
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src="https://code.jquery.com/jquery-3.4.1.js"
integrity="sha256-WpOohJOqMqqyKL9FccASB9O0KwACQJpFTUBLTYOVvVU="
crossorigin="anonymous"
></script>
<script
src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
crossorigin="anonymous"
></script> -->
<!-- <link rel="stylesheet" href="css/styles.css?v=1.0" /> -->
<link rel="stylesheet" href="bootstrap.min.css" />
<link rel="stylesheet" href="bootstrap-theme.min.css" />
</head>
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