Abhishek Kognole (@aakognole) header
Abhishek Kognole (@aakognole) profile picture

Abhishek Kognole

@aakognole

Researcher 👨‍🔬 Engineer 👨‍🏭 Explorer 🚙

aakognole.github.io/
Joined August 2009
  • Tweets276
  • Following278
  • Followers154
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Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)Photo by Abhishek Kognole (@aakognole)
Abhishek Kognole retweeted
SilcsBio (@silcsbio) profile picture
SilcsBio@silcsbio11 Mar 2025
ACS Spring 2025 is just two weeks away! The SilcsBio team will be in San Diego! We’ll be at the ✅ Expo with a booth, plus we have a✅ talk and a ✅ poster session lined up. Stay tuned for details on our schedule. If you’re attending, let’s connect! 👥 #CompChem #ACSSpring2025
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Abhishek Kognole retweeted
CHARMM-GUI (@CharmmGui) profile picture
CHARMM-GUI@CharmmGui21 Nov 2023
CHARMM-GUI now supports covalent ligand modeling:
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Abhishek Kognole retweeted
Alex MacKerell (@alex_mackerell) profile picture
Alex MacKerell@alex_mackerell10 Sep 2023
Nice review! The SILCS approach has been extended to model small molecule permeability; it is very fast, yields absolute FE profiles (not PMFs) and accurate permeabilities in conjunction with AI. See doi.org/10.1021/acs.jctc.1c0… and doi.org/10.1021/acs.jcim.3c0…
Image from Alex MacKerell (@alex_mackerell)
JCIM & JCTC Journals (@JCIM_JCTC) profile pictureJCIM & JCTC Journals@JCIM_JCTC10 Sep 2023
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice? #MolecularModeling #compchem pubs.acs.org/doi/10.1021/acs… #JCIM Vol63 Issue15 #Perspectives
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They...

Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They...

Abstract. Predicting from first-principles the rate of passive permeation of small molecules across the biological membrane represents a promising strategy

pubs.acs.org
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Abhishek Kognole retweeted
SilcsBio (@silcsbio) profile picture
SilcsBio@silcsbio31 Aug 2023
Tune in to our webinar in partnership with C&EN, discussing the trade-off between speed and accuracy in computer-aided drug design, highlighting the SILCS methodology. #compchem #drugdesign #CADD connect.discoveracs.org/CENW…

Overcoming the Trade-Off Between Speed and Accuracy in Computer-Aided Drug Design

connect.discoveracs.org
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Abhishek Kognole retweeted
SilcsBio (@silcsbio) profile picture
SilcsBio@silcsbio11 Aug 2023
Check out the recent article that highlights a novel covalent drug design workflow employing SILCS. This methodology holds immense potential for optimizing covalent drug interactions and target binding. #compchem #cadd #drugdesign pubs.acs.org/doi/10.1021/acs…
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😇 Lifesaver code in #compchem
Justin Lemkul (@JustinLemkulVT) profile pictureJustin Lemkul@JustinLemkulVT4 Jul 2023
Happy to have this one out, a labor of love for many years since my postdoc, transformed through the efforts of András Wacha. I present: charmm2gmx, a totally rebuilt utility for porting the #CHARMM FF into GROMACS format. doi.org/10.1021/acs.jcim.3c0…

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

Abstract. CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation eng

pubs.acs.org
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Protein Charge Prediction - Another application of SILCS approach, a multifaceted technology in computer-aided drug design. Nice work @AsukaOrr @alex_mackerell #CompChem #Biologics #SILCS @silcsbio doi.org/10.1021/acs.molpharm…
Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein...

Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein...

Abstract. Protein-based therapeutics typically require high concentrations of the active protein, which can lead to protein aggregation and high solution v

pubs.acs.org
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Come see us @silcsbio at booth 418 at ACS Spring 2023 Expo! Stop by my poster on SILCS-RNA tonight. #ACSSpring2023 #COMP #compchem #drugdesing
Image from Abhishek Kognole (@aakognole)
Image from Abhishek Kognole (@aakognole)
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Really happy to see prompt action by @BaltimoreDPW on cleaning a dirty alley next to my new house. BALTIMORE CITY 311 app is very easy helpful. #Baltimore
Image from Abhishek Kognole (@aakognole)
Image from Abhishek Kognole (@aakognole)
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Thanks for sharing! #compchem doi.org/10.1021/acs.jctc.2c0…

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

Abstract. RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular

pubs.acs.org
PharmSci_Maryland (@PharmSci_UMB) profile picturePharmSci_Maryland@PharmSci_UMB6 Sep 2022
Kognole, Hazel and MacKerell extend the #SILCS technology to RNA showing the potential utility of the method for identifying novel ligand binding sites and facilitating the optimization of drug-like molecules. doi: 10.1021/acs.jctc.2c00381 @umsop @alex_mackerell
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Now you can start simulating N- and O-Linked glycopeptides and glycoproteins with #Drude FF. Check out our recent paper in @JPhysChem B. #compchem #glycotime #CHARMM #moleculardynamics @alex_mackerell pubs.acs.org/doi/10.1021/acs…
Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O‑Linked Glycopeptides...

Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O‑Linked Glycopeptides...

Abstract. Molecular dynamic simulations are an effective tool to study complex molecular systems and are contingent upon the availability of an accurate an

pubs.acs.org
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And I just found out that this good news comes on World RNA Day - August 1st! #ThereIsADayForThat 😇The codon AUG is the most common START codon, the first codon in the transcribed mRNA that undergoes translation. #WorldRNADay #RNAday #RNA
Abhishek Kognole (@aakognole) profile pictureAbhishek Kognole@aakognole1 Aug 2022
Really excited to share our work on development of SILCS-RNA, a structure-based drug design platform for targeting RNAs with small molecules, now published in ACS JCTC. doi.org/10.1021/acs.jctc.2c0… #RNA #SmallMolecules #DrugDiscovery #DrugDesign #SBDD #CADD #CompChem

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

Abstract. RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular

pubs.acs.org
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Really excited to share our work on development of SILCS-RNA, a structure-based drug design platform for targeting RNAs with small molecules, now published in ACS JCTC. doi.org/10.1021/acs.jctc.2c0… #RNA #SmallMolecules #DrugDiscovery #DrugDesign #SBDD #CADD #CompChem

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

Abstract. RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular

pubs.acs.org
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Congratulations to Dr. @PayalChatterj14 on a successful defense! And cheers to the great a mentor @alex_mackerell! #MackerellLab #UMB #PhDone
Image from Abhishek Kognole (@aakognole)
Image from Abhishek Kognole (@aakognole)
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Happy to join the team @earlycharm! bit.ly/3yl070S
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#compchem
Anmol Kumar (@anmol_aaryan) profile pictureAnmol Kumar@anmol_aaryan11 Feb 2022
We are delighted to share our work on automated prediction of electrostatic parameters using neural network model in the context of #Drude #Polarizable #ForceField. This work forms the backbone of generalizing Drude FF to novel drug like molecules. #DGenFF pubs.acs.org/doi/10.1021/acs…
Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical...

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical...

Abstract. The Drude polarizable force field (FF) captures electronic polarization effects via auxiliary Drude particles that are attached to non-hydrogen a

pubs.acs.org
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Thinking that using a polarizable forcefield could help solve your problem but don't know how to use it... Checkout @CharmmGui Drude Prepper with more info in our recently published paper in JCC. @WileyCTChem #compchem doi.org/10.1002/jcc.26795
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Glad to be a part of this amazing tool... Long live CHARMM-GUI! #compchem #charmmgui #HeyDrude
CHARMM-GUI (@CharmmGui) profile pictureCHARMM-GUI@CharmmGui7 Dec 2021
CHARMM-GUI Drude Prepper for molecular dynamics simulation using the classical Drude polarizable force field (with @aakognole @alex_mackerell): doi.org/10.1002/jcc.26795
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Abhishek Kognole retweeted
NYT Science (@NYTScience) profile picture
NYT Science
@NYTScience1 Dec 2021
This simulation provides an unprecedented glimpse at how the coronavirus survives in the open air as it spreads to a new host nyti.ms/3DaQrVx
The Coronavirus in a Tiny Drop (Published 2021)

The Coronavirus in a Tiny Drop (Published 2021)

A new simulation shows how the virus survives inside tiny airborne particles of water — and gives clues about how the Delta variant became dominant.

nytimes.com
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Congrats to @alex_mackerell on winning the @AmerChemSociety Award for Computers in Chemical and Pharmaceutical Research! cen.acs.org/people/awards/AC…
Image from University of Maryland School of Pharmacy (@umsop)
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