BOL: Related items

Foldit: Solve Puzzles for Science

Robert M Willioms — Thu, 21 Dec 2017 15:17:47 -0600

Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with the UW Department of Biochemistry. The objective of Foldit is to fold the structures of selected proteins as perfectly as possible

https://fold.it/portal/

Address of the bookmark: https://fold.it/

Protein-Protein Interaction Sites Predictions !

Poonam Mahapatra — Wed, 25 Apr 2018 04:53:20 -0500

The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues participating in a given PPI. Information about a protein’s interaction partners allows scientists to construct protein interaction networks, such as signaling pathways, which in turn facilitate the understanding of many biological and clinical observations.

Following are the list of tools commonly used to PPIs predictions:

Protein-Protein Interaction Sites

PPISP

A consensus neural network method for predicting protein-protein interaction sites

HOMCOS

A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

HotPOINT

Prediction of protein interfaces using an empirical model

ISIS

Prediction of interaction hotspots from sequence

KFC server

Automated decision-tree approach to predicting protein-protein interaction hot spots

meta-PPISP

A meta server for predicting protein-protein interaction sites. meta-PPISP is built on three individual web servers: cons-PPISP, PINUP, and Promate

ODA

Identification of optimal surface patches with the lowest docking desolvation energy values

PINUP

Protein binding site prediction with an empirical scoring function

Other Sites (DNA, RNA, Metals)

CHED

Web server for predicting soft metal binding sites in proteins

DBD-Hunter

A knowledge-based method for the prediction of DNA-protein interactions

DISPLAR

Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA using neural network method

iDBPs

Predicts DNA binding proteins for proteins with known 3D structure.

PFplus

A tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

FANTASIA

BioStar — Wed, 20 Aug 2025 02:48:15 -0500

FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from a PostgreSQL database with pgvector, to associate Gene Ontology (GO) terms with proteins.

https://www.nature.com/articles/s42003-025-08651-2

Address of the bookmark: https://github.com/CBBIO/FANTASIA

XAMPP: Starting Apache fail Ubuntu

Ram Yash Pal — Sat, 07 Jun 2014 05:52:35 -0500

Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php

Bioinformatics Made Easy Search: Bioinformatics tools and run genomic analysis in the cloud

Rahul Nayak — Thu, 20 Aug 2015 02:21:20 -0500

InsideDNA makes hundreds of bioinformatics tools immediately available to run via an easy-to-use web interface and allows an accurate search across all functions, tools and pipelines.

With InsideDNA, you can upload and store your own genomic/genetic datasets in a limitless cloud space, and instantly analyze it with a powerful compute instance, without any tool installation or set up hassle.

More at https://insidedna.me/

Address of the bookmark: https://insidedna.me/

Apache server setting !

Abhi — Fri, 29 Oct 2021 04:29:51 -0500

Apache is an open source web server that’s available for Linux servers free of charge.

In this tutorial we’ll be going through the steps of setting up an Apache server.

What you’ll learn

How to set up Apache
Some basic Apache configuration

Address of the bookmark: https://ubuntu.com/tutorials/install-and-configure-apache#3-creating-your-own-website

Heatmap Draw !

BioStar — Mon, 06 Mar 2023 04:24:57 -0600

Server for heatmap generation !

https://software.broadinstitute.org/morpheus/

Address of the bookmark: https://software.broadinstitute.org/morpheus/

QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.

Neel — Wed, 01 Apr 2020 10:30:52 -0500

Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair does not necessarily mean the lack of interaction. Indeed, recent studies, both computational and experimental, highlighted the promiscuity of both proteins and small molecules: many drugs have side effects i.e. they target proteins other than those known in public databases; and many proteins bind chemicals other than those known, opening the way to design repurposable drugs, new chemicals, or polypharmacological treatments.

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa210/5813333

Address of the bookmark: http://quartata.csb.pitt.edu/

htop explained

Jit — Wed, 06 Jul 2022 01:28:09 -0500

For the longest time I did not know what everything meant in htop.

I thought that load average 1.0 on my two core machine means that the CPU usage is at 50%. That's not quite right. And also, why does it say 1.0?

I decided to look everything up and document it here.

Address of the bookmark: https://peteris.rocks/blog/htop/

UK executive accused in GlaxoSmithKline China probe

phu — Wed, 14 May 2014 04:55:42 -0500

Mark Reilly and two other colleagues are also suspected of bribing government officials in Beijing and Shanghai, they said.

Police have handed the case over to prosecutors, officials said.

GSK said it took the allegations "very seriously" and would co-operate with the authorities over the matter.

Chinese authorities announced in July last year that they were investigating GSK, detaining four Chinese GSK executives.

http://www.bbc.com/news/world-asia-china-27403914