Shozeb Haider @shozeb_haider Twitter profile

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Shozeb Haider

2 years

Perhaps it’s wise to approach the subject cautiously. #thermodynamics #statisticalmechanics #AcademicTwitter #AcademicChatter

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Shozeb Haider

@shozeb_haider

5 months

We have a new minted PhD graduate from our lab at @School_Pharmacy . What makes this day even more special is that her first paper was also accepted today in @MedChemRes (more on that later) Congratulations Dr Abeer @abeeralanaziucl

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Shozeb Haider

@shozeb_haider

1 month

After reading about what Alphafold3 can do all day yesterday, I have designed a series of 10 attempts (max daily limit) that I will try out today. I shall push AF3 limits on non-canonical nucleic acids-protein complexes. Will keep posting results as they appear.

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Shozeb Haider

@shozeb_haider

6 years

Who did this ? #babas

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Shozeb Haider

@shozeb_haider

2 years

Both junior boys and girls champions at US Open 2022 are from @rnadalacademy . Now how cool is that.

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Shozeb Haider

@shozeb_haider

3 months

Telomeres are complicated structures that include multiprotein complexes and non-canonical nucleic acid structures. My recently graduated student @abeeralanaziucl reviews them from a structural perspective. @School_Pharmacy

Structural Motifs at the Telomeres and Their Role in Regulatory Pathways

Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

1 year

I find it odd when authors on MD papers mention that data is available on request, yet they have all sorts of excuses not to share the data. Data deposition prior to publication should be mandatory. Editors of open access journals please note. #openaccess #moleculardynamics

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Shozeb Haider

@shozeb_haider

2 years

My mother tells me that He was amazed when I went after the pen in his pocket instead of his glasses on my first meeting with him as a 1 yr old.

Syed Ubaidur Rahman

@syedurahman

2 years

Professor Irfan Habib, Professor Emeritus at AMU, has been made Honorary Fellow of New College, Oxford from where he had done his D.Phil. His books include: The Agrarian System of Mughal India 1556–1707 An Atlas of the Mughal Empire The Economic History of Medieval India etc

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Shozeb Haider

@shozeb_haider

4 years

No one wants to be left behind. @AcademicChatter #AcademicTwitter #AcademicChatter

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Shozeb Haider

@shozeb_haider

3 years

Our latest collaborative work on allosteric communication in Class A β-lactamases is out in @eLife

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Shozeb Haider

@shozeb_haider

4 years

Working from home ? - via Twitter #AcademicChatter #AcademicTwitter

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Shozeb Haider

@shozeb_haider

26 days

@nelsabbey My offence to this placard was that Dame Preeti Patel was not included.

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Shozeb Haider

@shozeb_haider

2 years

TMPyP4 stabilises DNA quadruplexes but also unfolds RNA quadruplexes. In our latest work, published in @J_A_C_S we show how this happens. @School_Pharmacy @ucl_arc @BristolChem @unige_en @ucl

Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex

The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 can have both a stabiliz...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

2 years

What an amazing read. The graphical history of the PDB. #pdb

Seeing the PDB

Ever since the first structures of proteins were determined in the 1960s, structural biologists have required methods to visualize biomolecular structures, both as an essential tool for their...

www.jbc.org

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Shozeb Haider

@shozeb_haider

4 months

If you ever embark on studying Holliday junctions at telomeres using single-molecule FRET, then you might want to look at a protocol we ( @abeeralanaziucl and Prof Gary Parkinson) developed using @oniHQ Nanoimager. Now out in @MedChemRes @School_Pharmacy

The use of single-molecule FRET for the characterization of Holliday junctions containing human...

Medicinal Chemistry Research - Single-molecule analysis has emerged as a powerful biophysical technique, allowing the investigation of molecular interactions at unprecedented spatial resolutions....

link.springer.com

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Shozeb Haider

@shozeb_haider

3 years

Our comprehensive work describing all known ligand binding sites on β-coronavirus main protease. Published in ⁦ @JCIM_ACS ⁩ #covid19

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

7 months

Nov 2nd, 1917. The root cause of all problems #BalfourDeclaration

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Shozeb Haider

@shozeb_haider

2 years

Our latest paper in @J_A_C_S led by the super talented @howorka_lab on DNA nanopores in membranes @School_Pharmacy @ucl_arc @ucl Triggered Assembly of a DNA-Based Membrane Channel

Triggered Assembly of a DNA-Based Membrane Channel

Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics’ value for science and technology yet is...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

4 years

From all the noise, @barbaraslavin1 gives the best explanation

CBS Mornings

@CBSMornings

4 years

Here to discuss the consequences of the death of Soleimani: The director of the Atlantic Council’s, “Future of Iran” initiative @barbaraslavin1

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Shozeb Haider

@shozeb_haider

2 years

23 years, over 50 publications and G-quadruplexes between us. @School_Pharmacy

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Shozeb Haider

@shozeb_haider

2 years

Biomolecular simulations at @CCP5UK summer school 2022.

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Shozeb Haider

@shozeb_haider

1 month

The tweeds of the day . @TweedRun @School_Pharmacy @DrZoeWaller

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Shozeb Haider

@shozeb_haider

3 years

I think my protein is a split personality (and has a pretty cool hair do) #ProteinImager #PDB50 @buildmodels

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Shozeb Haider

@shozeb_haider

3 years

No trials, no studies to support it. Efficacy data for adult usage yet to be published and now some expert panel approves #Covaxin usage in children. Astonishing how approval works in India.

NDTV

@ndtv

3 years

#Covaxin , #coronavirus

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Shozeb Haider

@shozeb_haider

1 month

Is it possible to make sense of evolutionary patterns in highly conserved enzymes using dynamics? Here we use deep learning to study the L2 family of β-Lactamases. @School_Pharmacy @CWRUSOM @JCIM_JCTC

Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning

L2 β-lactamases, serine-based class A β-lactamases expressed by Stenotrophomonas maltophilia, play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

4 years

The Pfizer vaccine was developed by #BioNTech . A German company started by two Turkish Immigrants - Uğur Şahin and Özlem Türeci in 2008. It just could be some immigrant who might come to our rescue. #coronavirusvaccine

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Shozeb Haider

@shozeb_haider

3 years

My alma mater.

Upasana

@U_pasana

3 years

Restoration of Constantia, home of Claude Martin in Lucknow, now La Martiniere (est.1845) accomplished by Dr Neeta Dass conservation architect with help from school alumni. Painting work by local restoration artist Ansar-ud-din #Architecture #Heritage

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Shozeb Haider

@shozeb_haider

3 years

The beauty of #Deepmind Alphafold DB is that it has now permanently taken care of those short missing loops from the experimentally solved structures. They were such a nuisance to model before starting any simulation.

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Shozeb Haider

@shozeb_haider

5 years

No more memory issues in visualising MD trajectories. Using ⁦ @mdanalysis ⁩ and #pymol . Excellent tool from ⁦ @lorenz_lab ⁩

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Shozeb Haider

@shozeb_haider

1 month

I read a lovely post on how AF3 can predict electrolyte RDFs. So I digress from protein-NA complexes to just NA complexes. (Will come back to it) Case 3: 1JRN oxytricha bimolecular G4T4G4. My fav since I solved it. Perfect prediction with loops and 5 ions.

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Shozeb Haider

@shozeb_haider

5 years

Probably the best riverfront in all of India

Tamheed Bukhari

@tamheedbukhari

5 years

An evening view of Jhelum.

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Shozeb Haider

@shozeb_haider

2 years

Bumped into a physicist this afternoon. #london

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Shozeb Haider

@shozeb_haider

3 years

My dear #keshavdesiraju you will be dearly missed. Trips to Paudhar will never ever be the same again.

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Shozeb Haider

@shozeb_haider

3 years

What a delight to be back around colleagues at the @School_Pharmacy Teaching away day.

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Shozeb Haider

@shozeb_haider

1 year

A wonderful lunch date with Dr Rosie Llewellyn-Jones. Historian, Author and an expert on all things about #Lucknow .

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Shozeb Haider

@shozeb_haider

3 years

#Srebrenica

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Shozeb Haider

@shozeb_haider

8 years

And here is a pic I took recently @MrHusayn @IraqiPic @Iraqesque #malwiya

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Shozeb Haider

@shozeb_haider

6 years

@IndiaExplained Modi would never forget how the press cornered him on his first visit to UK. He wouldn’t dare have an open session in a university. Only prescreened fans at Wembley.

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Shozeb Haider

@shozeb_haider

4 years

€9500 per article. Scientific publishing is broken #AcademicTwitter #AcademicChatter

Nature journals announce first open-access agreement

Nature - The arrangement will allow some researchers in Germany to publish openly — but critics say it comes with a high price.

www.nature.com

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Shozeb Haider

@shozeb_haider

1 month

Last of the day has to be our latest structure due to come out any time now. Not seen yet by AF3 Case 10: 8AYG the first intramolecular ILPR iMotif The C-stem is predicted correctly, but again the loops are just collapsed on the stem. Not quite right.

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Shozeb Haider

@shozeb_haider

1 month

The most important part is the junction. There are certain structural rules that govern how and what sequences form the junction. They all break down in the AF3 prediction (pink).

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Shozeb Haider

@shozeb_haider

2 years

@nanome_inc exhibit has to be the best at #bps2022 Do check the models in VR

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Shozeb Haider

@shozeb_haider

1 month

we know from experiments that telomeric G4 can adopt multiple topologies Case 5: 2HY9 Incorrect prediction. The strand polarity changes and AF3 pushes towards propeller instead of hybrid1

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Shozeb Haider

@shozeb_haider

1 month

As a result, AF3 (pink) is clueless about the base pairing. It randomly starts placing bases. An incorrect purine:pyrimidine swap occurs.

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Shozeb Haider

@shozeb_haider

2 years

Just a tweet of appreciation for my local councillor @NeilGarratt for paying attention to his constituent’s issues. #Sutton

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Shozeb Haider

@shozeb_haider

6 years

Even better - This advert should be spammed into every Indian Whatsapp account in multiple languages @waglenikhil

nikhil wagle

@waglenikhil

6 years

Today WhatsApp has given full page advertisement about how to fight fake news. This advertisement should be published in regional languages too.

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Shozeb Haider

@shozeb_haider

6 years

Here I give you ⁦ @Imamofpeace ⁩ aka the #fakesheikh . Didn’t take long to track that one ⁦& btw Tommy Robinson, rw British islamophobe criminal is his hero @t_d_h_nair ⁩ ⁦ @khanumarfa ⁩ ⁦ @iamrana ⁩ ⁦ @irenaakbar ⁩ ⁦ @OmairTAhmad ⁩

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Shozeb Haider

@shozeb_haider

1 month

Case 1: PDB 2QNC. A DNA Holliday junction in complex with T4 endo IV resolvase. Amazingly AF3 predicts the complex within 1.3A. The protein is spot on although one arm is slightly splayed outwards. Not unexpected as this protein was used in training. Pink-AF3 Green-2QNC

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Shozeb Haider

@shozeb_haider

5 years

This is by far the grandest mosque in the whole of Xinjiang. The interiors are exquisite.

Photos of Silk Road

@PicsSilkRoad

5 years

The Ceiling of Altun Mosque. Yarkand, Xinjiang/East Turkestan, China, Silk Road. #silkroad #NGSilkRoad

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Shozeb Haider

@shozeb_haider

2 years

Our latest work on identifying druggable cryptic pockets on #NSP1 in #SARS -CoV2 and other beta coronavirus. We back our prediction using X-ray crystallography paving way for structure-based drug design. Led by @gervasiolab Frank Kozielski and teams

Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simula...

A combination of simulations and experiments was used to discover druggable cryptic pockets in non-structural protein 1, a promising but difficult target for coronaviruses, indicating a viable drug...

elifesciences.org

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Shozeb Haider

@shozeb_haider

3 months

Excellent talk on computational approaches to study biomolecular systems by @lab_colombo . Hosted by @AriannaFornili and @ccpbiosim

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Shozeb Haider

@shozeb_haider

3 years

If you want to understand what has caused this Covid catastrophe in India, then just read this thread 👇🏻 #NewIndia

Kill Bill Pandey

@Kill_BillPandey

3 years

#IndiaCOVID19Update TIMELINE OF THE COVID CATASTROPHE Why is India alone so badly affected by covid this time round? ◾March 2020: Fosun Pharma of China invests $135 million with BioNTech to collaborate and develop 300 million doses of mRNA vaccines.

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Shozeb Haider

@shozeb_haider

1 year

A wonderful delegation from @astar_research Singapore came over show casing some of the finest research they are doing.

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Shozeb Haider

@shozeb_haider

1 month

Will continue with complexes again.

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Shozeb Haider

@shozeb_haider

1 month

Customary work stop. @School_Pharmacy @DrZoeWaller @TweedRun

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Shozeb Haider

@shozeb_haider

1 month

This got me thinking: how about the human telomeric sequence that forms 6 different topologies Case 4: 1KF1 The intramolecular 21mer Pretty impressive so far.

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Shozeb Haider

@shozeb_haider

5 years

There’s another one in the neighbourhood called the Turpan kazakhana @PicsSilkRoad #silkroad

Photos of Silk Road

@PicsSilkRoad

5 years

Local mosque in Turpan, East Turkestan/Xinjiang, China, Silk Road. #silkroad #NGSilkRoad

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Shozeb Haider

@shozeb_haider

1 month

However, the DNA is a mess. AF3 pushes the strands up by 2 bp.

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Shozeb Haider

@shozeb_haider

5 years

War will never solve problems #NoToWar

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Shozeb Haider

@shozeb_haider

2 years

Ever wondered what DNA looks like? #DNA #nucleicacids

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Shozeb Haider

@shozeb_haider

4 months

A billionaire defending his wife of plagiarism, which he himself advocated to oust the president of Harvard is the most amusing thing happening in the academic world right now. Read his whims in the demand letter. Highly entertaining.

Bill Ackman

@BillAckman

4 months

Over my 35-year career, I have been the subject of many thousands of articles, including extremely negative, inaccurate, and libelous articles, yet I have never sued a media organization or a journalist. Beginning in early January of this year, Business Insider released a series

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Shozeb Haider

@shozeb_haider

2 years

What a fascinating article in @J_A_C_S Antigen-Triggered Logic-Gating of DNA Nanodevices @DNA_RNA_Uni

Antigen-Triggered Logic-Gating of DNA Nanodevices

Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state...

pubs.acs.org

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Shozeb Haider

@shozeb_haider

2 years

Teaching in VR with @nanome_inc @School_Pharmacy @hiltonlab

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Shozeb Haider

@shozeb_haider

3 years

Neighbours smashing it this Halloween.

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Shozeb Haider

@shozeb_haider

3 months

Our latest work “Modular synthesis of functional libraries by accelerated SuFEx click chemistry” in ⁦ @ChemicalScience ⁩. Led by John Moses and team at ⁦ @CSHL ⁩

Modular synthesis of functional libraries by accelerated SuFEx click chemistry

Accelerated SuFEx Click Chemistry (ASCC) is a powerful method for coupling aryl and alkyl alcohols with SuFEx-compatible functional groups. With its hallmark favorable kinetics and exceptional...

pubs.rsc.org

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Shozeb Haider

@shozeb_haider

1 year

It’s good to see old friends again #BPS2023

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Shozeb Haider

@shozeb_haider

8 years

@NickKyrgios The moment you realize you are not bigger than the sport, everything will fall in perspective #arrogance

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Shozeb Haider

@shozeb_haider

2 years

And so ends #EMBOFuncNucleicAcids with a gala dinner. Lovely to see old colleagues and friends. Thank you @ambadasrode

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Shozeb Haider

@shozeb_haider

4 years

I truly believe the business of scientific publishing is broken. #AcademicChatter

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Shozeb Haider

@shozeb_haider

1 month

What if I trick AF3. Change a BrU to T in one of the bimolecular structures which AF3 has never seen before. Case 7: 1K8P bimolecular human telomeric G4 AF3 goes crazy. It now predicts 2 hexads and 1 AT tetrad.

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Shozeb Haider

@shozeb_haider

2 years

@HeathrowAirport A suggestion: given the current situation at the airports, you should give an hourly update of Security and immigration queues or get a live tracker on your website. #heathrow

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Shozeb Haider

@shozeb_haider

2 years

The Dons of the #Quadruplex world descend on @unescorcb , Faridabad in 2 days time. What an amazing line up of speakers at great organisational work by @ambadasrode #EMBOfuncNulceicAcids

Functional nucleic acids: Recent landscapes and therapeutic applications

Advances in instrumentation and methodology have allowed researchers to identify the functions of nucleic acid beyond their canonical roles as genetic material. The programmability and biocompatibili…

meetings.embo.org

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Shozeb Haider

@shozeb_haider

9 years

Most handsome Zafar portrait from the #HowardHodgkin collection 24.10.1775-7.11.1862 @DalrympleWill @BL_VisualArts

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Shozeb Haider

@shozeb_haider

6 years

What a pigeon house!!!

Photos of Silk Road

@PicsSilkRoad

6 years

Inside the centuries-old Pigeon Tower of Meybod, Iran, Silk Road. #silkroad #NGSilkRoad

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Shozeb Haider

@shozeb_haider

3 years

@kittusen Clearly you haven’t been to La Martiniere, Lucknow

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Shozeb Haider

@shozeb_haider

4 months

Our latest work in collaboration with Neidle group on G-quadruplex-targeting clinical candidate QN-302 & analogs. QN-302 was given IND clearance by FDA to initiate Phase 1a clinical trials for Pancreatic Cancer ⁦ @School_Pharmacy ⁩ ⁦ @QualigenTx ⁩

Structure–activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two...

Scientific Reports - Structure–activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular...

www.nature.com

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Shozeb Haider

@shozeb_haider

1 month

The ions are perfectly placed.

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Shozeb Haider

@shozeb_haider

1 month

How does it fare with bimolecular telomeric RNA Case 6: 3IBK Telomeric RNA The G4 backbone fits well, however there is a bit of wobbling of bases in the loops. So far, so good since the model would be trained on these systems.

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Shozeb Haider

@shozeb_haider

4 years

If I submit an article to the Int Journal of Secret Agents then do I need to provide an author list? #JustAsking @AcademicChatter

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Shozeb Haider

@shozeb_haider

2 years

Speak up against fake medicines where ever you are. Read all about #FightTheFake here. Excellent work @OksanaPyzikUCL and @ProfIAbubakar

Nature Reviews Disease Primers

@DiseasePrimers

2 years

In this Comment, @OksanaPyzikUCL and @ProfIAbubakar discuss the impact of circulating falsified medicines, particularly on the African continent, and that a global, cross-border response is needed to reduce extensive humanitarian and economic harm.

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Shozeb Haider

@shozeb_haider

4 years

@theBekku Coding? That’s so year one.

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Shozeb Haider

@shozeb_haider

2 years

Congratulations @dikshaparwanaa on winning the first prize for flash talks. Not a bad start for your first conference. #EMBOfuncNucleicAcids

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Shozeb Haider

@shozeb_haider

4 years

Remembering Girish Karnad on his birthday. India’s finest playwright.

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Shozeb Haider

@shozeb_haider

2 years

Our latest work on the the cryptic pockets in NSP1 using MD and validation through X-ray crystallography. It’s the first such structure of NSP1+fragment, opening avenues for structure-based drug design #covid19 #nsp1

Gervasio's Research Group (Protein Dynamics)

@gervasiolab

2 years

Our preprint on cryptic pockets in coronavirus Nsp1 is now on @biorxivpreprint We combined SWISH, MD and Xray to reveal the pockets. Many thanks to @shozeb_haider , @c3starellas , @igaldadas , @albertobors and Frank Kozielski for the successful collaboration!

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Shozeb Haider

@shozeb_haider

5 years

My PhD student Aishat giving her talk on structure-based enzyme engineering #uclpharmphd19 @School_Pharmacy

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Shozeb Haider

@shozeb_haider

2 years

Had a great time at #ullasummerschool2022 with @gervasiolab and @igaldadas . Time to head back from #Uppsala . See you all in Leiden. @ullanetwork

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Shozeb Haider

@shozeb_haider

4 months

It’s been a good day today for publications from our group. Two papers accepted with minor and one subject to major corrections.

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Shozeb Haider

@shozeb_haider

1 month

Case 2: what happens if you change the sequence of DNA to equal length? The protein again is perfectly predicted, however the DNA becomes long rods.

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Shozeb Haider

@shozeb_haider

8 years

@mithelesh @iamrana the churning of the ocean 'samudra manthan' in Khemer temples #Cambodia #khemer

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Shozeb Haider

@shozeb_haider

2 years

A full house at the @School_Pharmacy Research Away Day. Kick off by @DrZoeWaller

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Shozeb Haider

@shozeb_haider

2 years

Perfect for purine-ated cycles.

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Shozeb Haider

@shozeb_haider

5 years

Sadly no more. They are now banned.

Photos of Silk Road

@PicsSilkRoad

5 years

Driving a donkey cart. Hotan, Xinjiang/East Turkestan, China, Silk Road. #silkroad #NGSilkRoad

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Shozeb Haider

@shozeb_haider

5 years

My domestic help, who is from Gujarat & has made 2 appeals against her expired visa tells me she wants Brexit because there are too many Europeans here. #Brexit #oxymoron

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Shozeb Haider

@shozeb_haider

3 years

Our first preprint of the year; in collaboration with @AdrianMulholla1 and @gervasiolab . Happy to take suggestions. #lactamases

bioRxiv

@biorxivpreprint

3 years

Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics #bioRxiv

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Shozeb Haider

@shozeb_haider

1 month

What if I give it the telomeric G4-duplex hybrid that AF3 has never seen before. Case 9: 5DWX It predicts the duplex part and the G-Stem correctly but has no clue what to with the super important loops. However if I give it what it saw in training, it gives a perfect fit.

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Shozeb Haider

@shozeb_haider

3 years

And look who joined me in Goodenough College. Sir Syed Ahmad Khan. The founder of Aligarh Muslim University, India. My alma mater for my UG and PG courses #AMU @AMUofficialPRO

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Shozeb Haider

@shozeb_haider

2 years

A first hand account of molecular simulations by Prof Jorgensen @JorgensenWL #UCL

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Shozeb Haider

@shozeb_haider

1 month

Attempt 8, was wasted on 3SC8. I should have known better that all G4 structures with ND compounds will be predicted parallel stranded. What a cheap waste of precious resources :0) Oh well, on to the next difficult case.

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Shozeb Haider

@shozeb_haider

1 year

Our latest work on the dynamics of the tetrameric L1 metallo-β-lactamase. We show how gating interactions would control loop dynamics around the active site. @School_Pharmacy @cwru @ORNL

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lact...

Extremely significant interactions between α3-β7 and β12-α5 loops in the tetrameric L1 metallo-β-lactamase play an important role in the structural remodeling of the active site and offer insights...

elifesciences.org

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Shozeb Haider

@shozeb_haider

5 months

While the rest of us recover from 2023, the bar has been set really high by @DrZoeWaller and team on day 2 of 2024.

OBC

@OrgBiomolChem

5 months

📢Our first issue of 2024 is now online! Check out the #openaccess research behind the cover by Stephen Neidle, @DrZoeWaller & co @School_Pharmacy on how QN-302 has opposing effects between i-motif & G-quadruplex DNA structures in the S100P gene promoter

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