The Suns protein search engine lets you perform fast all-atom searches on protein structures
Note that the DeGrado lab hosts a public search engine which you can use for
free at suns.degradolab.org. The Suns PyMOL plugin and the suns-cmd
command line tool both will send searches to this public server by default and
if you are satisfied with that server you do not need to deploy your own server
using this source package.
The main reasons you might want to build this package and host your own search engine are:
-
You are a company that wants to host its own search service on a private intranet so that the search queries never leave your network
-
You want to customize the searchable motifs or protein structures
-
The server at
suns.degradolab.orgis unavailable
This package does not include either the Suns PyMOL plugin, nor the
suns-cmd command line search tool. Those are provided separately at:
PyMOLclient: https://doi.org/10.1371/journal.pcbi.1003750.s005suns-cmd: https://github.com/Gabriella439/suns-cmd
In order to deploy your own server, you must install the nix package manager,
which you can find here:
Then you must install the nixops deploy tool by running:
$ nix-env --install --attr nixops --file ./release.nixThis repository comes with a pdb/ subdirectory with one example PDB file
inside (2GBP.pdb). Before deploying the server you must populate this
directory with your desired set of PDB structures that you would like the SUNS
server to index and make searchable
Note that suns-server requires approximately 1 GB of working memory per 270
chains, so factor that into how many structures you want to be able to search.
If you're not sure what to use, try one of the PISCES datasets curated by the Dunbrack lab:
You can optionally change the set of motifs that Suns indexes, too. If you don't want to do that then skip this section.
A default motif directory is provided with a reasonable default set of motifs.
Each sub-directory corresponds to a searchable motif, and the PDB files
contained within these sub-directories correspond to specific instances of each
motif type.
You need at least one PDB file per residue type that the motif matches. For
example, the peptide_bond motif has one file per residue, since it matches all
twenty residue types. Each match must have the same number of atoms and the
atom order between matches must be consistent.
Also note that motifs are indexed by bonds, not by atoms. That means that you cannot define a single-atom motif and it also means that any non-bonded atoms will be ignored.
Note that if you are using the PyMOL plugin and choose to customize the
motif directory, you will also need to rebuild the PyMOL plugin to recognize
the new motifs you have chosen. This is because the PyMOL plugin uses the
motif definitions to automatically expand selections to motifs. See the
PyMOL plugin build instructions for details on how to customize its behavior.
This is set up so that you can use nixops to deploy the server. nixops
supports several deployment options, including (but not limited to):
- Deployment to an AWS EC2 instance
- Deployment to a VirtualBox virtual machine
- Deployment to a
libvirtdvirtual machine running on NixOS
The following sections explain how to deploy to the above types of machines
Note that nixops also supports deploying to an existing machine running NixOS,
but that's not covered in this manual
Also, if you have any issues with the following instructions, you might want to check out the NixOps manual:
The manual also includes instructions for additional ways that you can customize your deployment beyond the defaults configured in this repository
You will need to create an AWS account with programmatic access by following the instructions here:
... and then saving your credentials to ~/.aws/credentials, like so:
[default]
aws_access_key_id = AKIA...
aws_secret_access_key = ...
Make sure that this ~/.aws/credentials file is not world-readable!
Modify the nix/ec2.nix to specify the AWS region and instance size you want
to use. The deployment uses t2.micro by default, which is eligible for 750
hours of free tier usage.
Once you are done, you can run:
$ nixops create --deployment suns nix/ec2.nix nix/logical.nix
$ nix/deploy.shYou must first install VirtualBox from:
Modify nix/vbox.nix to configure how much memory (in MB) that you wish to
provide the virtual machine and then run:
$ nixops create --deployment suns nix/vbox.nix nix/logical.nix
$ nix/deploy.shFollow the instructions here to set up libvirtd on your NixOS machine:
Modify nix/virtd.nix to configure how much memory (in MB) that you wish to
provide the virtual machine and then run:
$ nixops create --deployment suns nix/virtd.nix nix/logical.nix
$ nix/deploy.shOnce the deploy completes the server is ready to go. You can obtain the server IP address by running:
$ nixops info --deployment suns... and once you point your PyMOL SUNS plugin to that IP address you can begin
searching for protein structures.
You can also log into the server by running:
$ nixops ssh --deployment suns machine... and you can turn off the machine by running:
$ nixops stop --deployment suns... and you can also destroy all traces of the instance or virtual machine by running:
$ nixops destroy --deployment suns
$ nixops delete --deployment sunsCopyright 2013-2017 Gabriella Gonzalez
This file is part of the Suns Search Engine
The Suns Search Engine is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
The Suns Search Engine is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with the Suns Search Engine. If not, see http://www.gnu.org/licenses/.