Sutanu Mukhopadhyay

🇮🇳
|| Computational aficionado || Research Scholar@SNBNCBS
#computationalchemistry #computationalbiology
#allostery #CADD

[Sutanu Mukhopadhyay @AItrovert]

Published online! 🙂

"A multidrug efflux protein in Mycobacterium tuberculosis; tap as a potential drug target for drug repurposing"
https://t.co/efwrWLY6AK

[Sutanu Mukhopadhyay @AItrovert]

You can talk to AI for 3 hours.
You can't make a 3-minute phone call.

We have introverts.
We have extroverts.
I think we need a new category:

AItroverts. 🤖
People who are more comfortable talking to AI than to people.

Are you an AItrovert?

#AItrovert #Introvert #AI

[Deniz Kavi @kavi_deniz]

Can't keep up with all the new computational tools? Here are the top ones to know for biology, chemistry and informatics

Bioinformatics

BLAST
MAFFT
Foldseek
MMseqs
Biotite
Biopython
Biopandas
RCSB PDB
UniProt
InterPro

𝘊𝘩𝘦𝘮𝘪𝘯𝘧𝘰𝘳𝘮𝘢𝘵𝘪𝘤𝘴 & 𝘴𝘮𝘢𝘭𝘭 𝘮𝘰𝘭𝘦𝘤𝘶𝘭𝘦𝘴

Chembl
Rdkit
Boltz-2
Pharmit (pharmacophore search)
AutoDock/GNINA
REINVENT
BindingDB
datamol & molfeat
GPCRdb

𝘈𝘯𝘵𝘪𝘣𝘰𝘥𝘺 𝘪𝘯𝘧𝘰𝘳𝘮𝘢𝘵𝘪𝘤𝘴

ANARCI
AbYsis
TAP
SabDab
PlabDab
AbodyBuilder/ImmuneBuilder
IgBlast
@tamarindbio Database & immune protein annotator
BioPhi

𝘗𝘳𝘰𝘵𝘦𝘪𝘯 & 𝘮𝘰𝘭𝘦𝘤𝘶𝘭𝘢𝘳 𝘥𝘦𝘴𝘪𝘨𝘯

AlphaFold2
Boltz-2
RFDiffusion
ProteinMPNN
PyRosetta
BindCraft
RFpeptides
Chai-1

𝘉𝘪𝘰𝘱𝘩𝘺𝘴𝘪𝘤𝘴 & 𝘥𝘺𝘯𝘢𝘮𝘪𝘤𝘴

GROMACS
OpenMM
OpenFE (+RBFE)
OpenFF
NAMD
AmberTools
PLUMED

Try out @tamarindbio to use (nearly) all of them, in a secure, scalable environment with no setup. required. On Tamarind, using our web interface or AI Copilot, you can connect all of the aforementioned tools together, deploy your custom tools, and create specialized versions for your own data.

[Yoshitaka Moriwaki @Ag_smith]

おーん　これいいっすね〜

[Sutanu Mukhopadhyay @AItrovert]

@sukritsingh92 Congratulations!

[Sann @san_x_m]

The most powerful companies on Earth were shaped, in part, by a small man wrapped in a blanket in a Himalayan village.

Steve Jobs went looking for him. Mark Zuckerberg was sent by Jobs to find him. He was already dead before either of them ever heard his name properly.

His name is Neem Karoli Baba.

He was born Lakshman Narayan Sharma, in a village called Akbarpur in Uttar Pradesh, around 1900. Little is recorded of his early life beyond what devotees have passed down. He left home as a teenager to live as a wandering ascetic, then returned to a settled life for a time, before taking up that path again.

Devotees say the name he became known by came from an incident on a train. He was travelling without a ticket near a village called Neeb Karori, and was made to get off. According to the story, the train would not move again until he was allowed back on board.

He eventually settled in the Kumaon hills of what is now Uttarakhand, and in 1962 built an ashram on the bank of the Kosi river, at a place called Kainchi Dham. He lived simply, sitting on a raised cot wrapped in a blanket, and taught almost nothing in the way of formal philosophy. Devotees describe his teaching as 2 words. Love, and service.

In the late 1960s and early 1970s, a handful of young Americans found their way to him. Among them was Richard Alpert, a Harvard psychologist who later became known as Ram Dass and wrote a book about the experience that reached readers across the world.

He died in Vrindavan on 11th September 1973.

The next year, a 19 year old college dropout named Steve Jobs travelled to India specifically hoping to meet him. He arrived at the ashram to find it nearly empty. Neem Karoli Baba had been dead for months.

Jobs never met him. He stayed in India anyway, and the trip is described in his authorised biography as shaping the simplicity and intuition that would later define his approach to building products.

Decades after that, Jobs told a younger entrepreneur to make the same journey. Mark Zuckerberg has said that when Facebook was going through a difficult period, before the News Feed existed, Jobs advised him to visit Kainchi Dham. Zuckerberg went, planned to stay a day, and stayed 2.

He has said the visit helped him think more clearly about what he was actually building.

Julia Roberts has said a photograph of him was part of what drew her toward Hinduism. Larry Brilliant, an epidemiologist who helped eliminate smallpox, was a devotee and later brought Larry Page and Jeffrey Skoll on the same pilgrimage.

Whether the events attributed to him were miracles is not something an outsider can verify, and devotees themselves describe them as beyond ordinary explanation. What can be verified is smaller, and in its own way just as strange.

A man who owned almost nothing, who left no written philosophy behind, is still quietly present in the founding stories of some of the companies that now shape how billions of people communicate.

[Suman Chakrabarty @SumanPhysChem]

Abstract submission is now open for our flagship national conference: Frontiers of Physical Chemistry (FPC 2026)

Dates: 28–31 October 2026
Venue: S. N. Bose National Centre for Basic Sciences, Kolkata

FPC 2026 is the flagship national conference of physical chemistry in India, bringing experimentalists, theorists and computational scientists together for four days in Kolkata.

Abstract submission deadline: 10 September 2026

Website: https://t.co/XtB1DJc6v9
Contact us: [email protected]

Please pass this on to the students and postdocs in your group. We are looking forward to host you at SNBNCBS, Kolkata.

Yours sincerely,
Conveners: Prof. Ranjit Biswas (SNBNCBS) and Prof. Suman Chakrabarty (SNBNCBS)
Co-conveners: Prof. Ayan Datta (IACS), Prof. Amit Kumar Paul (Bose Institute), and Prof. Susmita Roy (IISER Kolkata)

[Sutanu Mukhopadhyay @AItrovert]

স্বতন্ত্রতা দিবসের শুভেচ্ছা। 🌼
বন্দে মাতরম।

[Prism Science @PrismScienceOrg]

Most structures in the PDB report one set of coordinates. The experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble. New work recovers that hidden signal at scale in over 60,000 structures. https://t.co/kmIZdG3G9S

[Suman Chakrabarty @SumanPhysChem]

Happy to share a Feature Article (Perspective/Review) just published in @ChemCommun on "Computational strategies for allosteric drug discovery: from cryptic pocket detection to rational design".

Read here: https://t.co/0piaBctGbC

Thanks to my student Sutanu Mukhopadhyay @SUTANU71933293 for his hard work in putting this together.

[Dr. Anirban Ganguly (অনির্বাণ গঙ্গোপাধ্যায়) @anirbanganguly]

A most moving and inspiring tribute to Dr Syama Prasad Mookerjee penned by Prime Minister Shri @narendramodi on his 125th birth anniversary, published in all dailies across the country…

“There are moments in history when an individual's final sacrifice transcends politics and enters the realm of national memory.”

https://t.co/ol1fHyVNrF

#SyamaPrasadMookerjee @125

[Yasin Polat @iamyasinpolat]

AlphaFold3 transformed protein structure prediction. However, it generally predicts a single static conformation.

A new Nature Biotechnology study addresses this using experimental guidance.

#AlphaFold3 #Bioinformatics #StructuralBiology

[Kresten Lindorff-Larsen @LindorffLarsen]

Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS

Thanks to Sören von Bülow, AF-CALVADOS is now on Colab

https://t.co/p8fIdPPZTz

[Narendra Modi @narendramodi]

I will be attending programmes in West Bengal over the next two days, the 20th and 21st. Tomorrow, 20th June, is special because we are marking Paschimbanga Divas. The programme for the same will be held in Tarakeswar in Hooghly district. The location is iconic due to its association with Dr. Syama Prasad Mookerjee and his efforts to preserve the culture of West Bengal. At Tarakeswar, various development works will be launched.

https://t.co/3GpD5FWbvX

[Yoshitaka Moriwaki @Ag_smith]

次世代PyMOLと噂の"patinae" (パティナ; formerly "PyMOL-RS")を使ってみている
https://t.co/aI0oltWuzM
9割くらいPyMOLな感じ　GPU特化しているだけあって描画がrayも含めて爆速
ちょっと配列の文字が見にくいとかあるけれどこれいいですね

[DSTIndia @IndiaDST]

On foundation day @snbkol celebrates four decades of nurturing scientific talent and advancing discovery.

Empowering students, researchers and innovators through world-class infrastructure, cutting-edge research and global collaborations, the institution continues to strengthen India's scientific sovereignty and innovation ecosystem.

As an autonomous institution under @IndiaDST, its journey is reinforced by @IndiaDST's strategic support for indigenous technologies, advanced computing and frontier research—driving the vision of an #AtmanirbharBharat built on knowledge, innovation and self-reliance. #FoundationDay

@DrJitendraSingh @rajesh_gokhale @Dhana_Arumugam1 @DBTIndia @CSIR_IND @moesgoi @mygovindia

[Anand Ranganathan @ARanganathan72]

Spine always grows in the back that is against the wall. America denied us crucial LOX/LH₂ cryogenic engine technology. We developed it indigenously and using it we now send American satellites into space.

India can remain sovereign only if it has a sovereign AI. @narendramodi

[Gautam R. Desiraju🇮🇳 @GautamDesiraju]

https://t.co/w9u1rWwLIU

[Vincent Alexander @NonsenseIsland]

RIP Marjane Satrapi, the great cartoonist and film director, best known for PERSEPOLIS. She was only 56. A great talent. She will be missed.

[Suvendu Adhikari @SuvenduWB]

Tomorrow at 11 AM, the full Cabinet of the democratically elected Nationalist State Government of West Bengal will be sworn in at the Lok Bhavan.
35 Ministers of the WB Govt will take their Oath of Office, administered by His Excellency; the Hon'ble Governor Shri R.N. Ravi Ji.
We stand committed to fulfilling the aspirations of the People of West Bengal.

[Hira_Labo🐻データサイエンス @hirat62363752]

Spatiotemporal graph neural networks reveal conformational binding signature in protein dynamics

タンパク質MDトラジェクトリからコンフォメーション特異的な特徴を抽出する時空間GNN
活性型構造の特徴を残基単位で同定

https://t.co/IVHgjMVEMJ
https://t.co/rtKce47Qri