RESEARCH NETWORK
ABOUT
"Reimagine cooperation" amongst scientists to solve problems which you never thought to attempt to consider due to enormous complexity and sheer scale. Our lab is disrupting barriers and rules in this age of social media and artificial intelligence to bring new level of co-operation between scientists. The scale shall be enormous and the rewards shall be huge.
The reason is very simple:
"Connections matter" – in terms of productivity, in terms of obtaining grants, in terms of promotion and advancement, and in terms of retention in academic positions, says a new Harvard-based study
Scientific collaborations & team science are more strikingly prevalent today than it was decades ago (Wuchty et al 2007). In many areas of biomedical science the trend is toward catalyzing collaborative efforts that bring together researchers with diverse scientific backgrounds and perspectives to address perplexing questions and solve complex problems that benefit from an interdisciplinary or multidisciplinary approach (2).
How about building a network of several hundred scientists and their respective teams to solve something massive ?
Here we present a challenge !
This website is a part of platform to build scientific collaborations to develop large scale docking pipeline for discovery of new drugs, vaccines; identification of side effects of drugs, & drug re-positioning.
Background:
This website also complement our ongoing effort in the area of building large scale computational frameworks to address bigger and complex problems (Rawal et al 2011, Jagannadham et al 2016). As a part of our work on obesity networks where we built a pipeline to dock drug(s) against the full proteome, we attempted to understand several important aspects in side effect predictions and network based therapeutics.
Now, we are carrying that work further to build a massive docking system which intends to employs best of the docking tools, scoring systems , and machine learning programs. Since, we need to understand what is available on molecular docking field, we started to prepare one of the most exhaustive review on molecular docking and its applications. This survey covers over 160 docking tools and their features, applications and limitations (Rawal et al 2019- Preprint).
Our work shows the use of machine-assisted literature mining to process and analyses huge amount of available information in reasonable time frame. With this work, we also propose to build a platform which combine human expertise (deep curation) & machine learning to participate in collaborative writing (i.e. review written by molecular docking tools developers/researchers) and also help them to collaborate in order to solve ambitious problems (i.e. building fast efficient docking system by combining best molecular docking tools or to perform large scale docking at human proteome level).
The title of this research article is " An extensive survey of molecular docking tools and their applications using text mining and deep curation strategies." The preprint version of this article shall be shared with you in case you want to participate or interested in the understanding more about this project.
VIDEOS
The small-world experiment actually comprised of several experiments conducted by Stanley Milgram and other researchers. Its aim was to examine the average path length for social networks of people in the United States.
What was innovative about this research? The fact that it suggested that human society is a small-world-type network characterized by short path-lengths.
These experiments are often associated with the phrase "six degrees of separation theory", but please note that Milgram never used this term himself
This lecture by Prof. Ernest Fraenkel is on protein interaction networks. He covers network models, including their structure and an analysis. He asks, "can we use networks to predict function?" He ends with a data integration example
lumen5-video-2.mp4Molecular docking is a method which predicts the preferred relative orientation of one molecule (key) when bound in an active site of another molecule (lock) to form a stable complex such that free energy of the overall system is minimized.