Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

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Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

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Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.

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Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)

While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].

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In this article. we are creating a pie chart of the docking score of five different compounds docked with the same protein. (more…)

One of the key questions surrounding online dating is whether these platforms lead to long-term relationships. Some 53% of adults under 30 have ever used a dating site or app – including a quarter who have used one in the past year. This compares with 37% of those ages 30 to 49 who have ever tried online dating and smaller shares of those 50 to 64 (20%) and 65 and older (13%) who say the same.

• “They are being tricked meeting up with people. And once they are getting there, they are actually taking money from them and things like that.”
• Additionally, male profiles that had a biography received 69 matches while those without received only 16 matches .
• There are also useful questionnaires that give you insight into your actually any traits and compatibility skills, which can help australia online dating game regardless of really hookup you end up using the most.
• According to Pew’s survey, 44 percent of online daters say they are looking for a long-term partner, 40 percent are interested in casual dating, 24 percent want casual sex, and 22 percent are just interested in friendship.

Pluralities also believe that whether a couple met online or in person has little effect on the success of their relationship. There are some groups who are particularly wary of the idea of meeting someone through dating platforms.

Tip 2: Build a genuine connection

Dating experts reveal the common blunders singles make with their photos, bios and prompts. Here are the new rules around ending a relationship by Zoom or texts. Furthermore, when describing themselves, people will often present their best selves while leaving out flaws. Some users may even deceptively present inaccurate information on their profile merely to get someone interested in them. Of course, hobbies and sports are always a great way to mingle. Consider joining a sports club or take lessons for an activity you want to start doing. Some people recommend Meet Upas a fun way to find people nearby who are interested in the same activities, whether that’s skating or going to museums or concerts.

The New Happy Has 500k Instagram Followers—Here’s How the Founder Built a Real Community

Once the quiz is completed, you fill out your profile with prompts, photos, and icons to indicate your hobbies and interest. Our tester says the profile took at least 20 minutes to complete, although not all users include the same level of detail on their profiles. Every Thursday, the app comes to life with people near you who also want to meet that day. In the time it takes to order a drink on one date, you’ll be matched with 3 users in your area that match your preferences. As sparks typically fly in just moments, these mini-dates save users time and energy–all from the comfort of your couch. We believe in quality over quantity, and that smart daily recommendations are better for busy people than an unlimited buffet of options. We let you set ultra-specific preferences and only suggest you a few Prospects a day that we think you will actually like.

A few of the best or cheapest competitors reaped significant gains while many former domestic champions or viable competitors lost out. These sites also generate significant levels of inequality, especially for men. One analyst found that“like inequality” for men on Tinderis higher than income inequality in the United States . Ananalyst at Hinge foundthat women’s inequality on that site was roughly equal to the average income inequality for the world’s countries (aGini coefficientof 0.376), similar to Western Europe.

Pure is a perfect match for those who value confidentiality, as profiles are removed every 24 hours. You can also send random pictures that will self-destruct a few seconds after your partner sees them. Even though Tinder claims to cater to all types of dating, everyone knows it’s best for one-night stands. Swipe right to meet people or left to remove them from your view. Priced at the higher $32 to $40 a month depending on age, all the Tinder Gold and Plus benefits are included at this tier.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)

With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn. (more…)

Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding IDs. (more…)

Due to the advancement of machine learning (ML) methods, we can find increasing applications of them in the field of bioinformatics as well. ML is being utilized in making personalized medicines, similarity searches in DNA and protein sequences, phylogenetics by mapping selected species on phylogenetic trees, gene and protein function annotation, generating chemical compounds, and so on. In this article, we will discuss an online database of ML-generated molecules known as cheML.io [1].

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Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)

In this article, we will obtain the secondary structure of multiple PDB files present in a directory using DSSP [1]. You need to have DSSP installed on your system. (more…)

After performing computational docking, a question that comes to mind most is “what docking score is considered good or bad”. In this article, we will discuss this in detail. (more…)

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

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Previously, we provided a Python script to download data over an FTP server. This article will use the Linux command to download multiple directories and subdirectories from an HTTPS server. (more…)

Openbabel [1] offers a wide range of operations. One of which is file format conversion which is most widely used. In this article, we will describe commands that convert file formats. (more…)

Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound. (more…)