@ForliLab

Molecular Modeling & Drug Design. The lab of Stefano Forli at Dept. of Integrative Structural & Computational Biology @scrippsresearch Home of the AutoDock

 La Jolla, CA (USA)
forlilab.org
Joined September 2018
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39Media
Important Update: we've decided to close our Twitter account because the increasing censorship and political controversies do not align with our values. You can continue following us on @forlilab.bsky.social. We will not post anymore here.
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Transthyretin’s structural asymmetry & “molecular breathing” drive its misfolding in ATTR—a discovery by Prof. Gabriel Lander (@LanderLab) & Prof. Jeff Kelly, published in @NatureSMB, that could inform new therapies for amyloid diseases. More: ow.ly/xCx850UVbbl
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Excited to announce the publication of our new paper on HIV-1 capsid stability!  cell.com/biophysj/fulltext/S… #HIV #MolecularDynamics
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Using atomistic molecular dynamics simulations, we explore how small molecules like PF74 and IP6 impact capsid stability. Our findings reveal that the tilt angle between neighboring hexamers plays a role in modulating stability, with implications for viral disassembly mechanisms.
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Kudos @ForliLab!!!
JCIM & JCTC Journals@JCIM_JCTC15 Nov 2024
#HighlightOfTheWeek Cosolvent molecular dynamics are an increasingly popular form of MD simulations where small molecule cosolvents are added to the system, helping to identify cryptic and allosteric pockets in proteins. #compchem pubs.acs.org/doi/10.1021/acs…
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Are you struggling to model your ligand into x-ray crystallography or cryo-EM density? Trying to dock a novel ligand into a well-studied target but just cannot get the pharmacophore position correct? Running a virtual screening and want to optimize your hit rate? (1/4)
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After almost 3 years of development and validation, we are pleased to announce our newest package in the AutoDock suite, CryoXKit! (2/4)
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Our pre-print with full method and validation details is also available on ChemRxiv: chemrxiv.org/engage/chemrxiv… (4/4)

Docking guidance with experimental ligand structural density improves docking pose prediction and...

Recent advances in structural biology have led to the publica- tion of a wealth of high resolution x-ray crystallography and cryo-EM macromolecule structures, including many complexes with small...

chemrxiv.org
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CryoXKit uses ligand density from x-ray crystallography and/or cryo-EM to guide dockings with AutoDock, resulting in better pose prediction and improved virtual screening performance across multiple systems. You can find the new tool now on GitHub: github.com/forlilab/CryoXKit (3/4)

GitHub - forlilab/CryoXKit: Tool to read crystallographic and cryo-EM files and interpolate density...

Tool to read crystallographic and cryo-EM files and interpolate density values onto a cartesian grid map - forlilab/CryoXKit

github.com
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Congratulations to Dr. @Batuujin for successfully defending his thesis yesterday! We are so proud of you and your work in our lab and in @WardLab1 . We can only look forward to the amazing science you will continue to do! #otop #sour_zebrafish
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If you’re interested in fast sampling and flexible and automated creation of cosolvent systems with @openmm_toolkit check this out! Huge thanks to the team @je_eberhardt @diogo_stmart @manuco17 @moonii1020 @Joe_r_loeffler @ForliLab pubs.acs.org/doi/10.1021/acs… ⚛️🧬

CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis

Abstract. Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated pr

pubs.acs.org
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Buried under a pile of docking data and not sure where to go next? Ringtail 2 will help you organize, filter, and visualize docking data via an easy-to-use command line tool, or integrated in your #python scripts using the brand new API! #autodockgpu #autodockvina
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Ringtail is available as an open-source package on PyPi, conda-forge, or by downloading and installing source code directly from GitHub (github.com/forlilab/Ringtail…). Installation instructions, usage examples, and extensive documentation are available here ringtail.readthedocs.io/en/l…

GitHub - forlilab/Ringtail: Package for storage and analysis of virtual screenings run with...

Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina - forlilab/Ringtail

github.com
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AlphaFold2+MD simulations = powerful insights into protein conformational ensembles, but can it capture all experimental structural variations? Great collaborative effort!! @Structure_CP @RRiccabona @OPIGlets @scrippsresearch @DTUtweet #compchem sciencedirect.com/science/ar…
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Mesoscale Explorer molstar.org/me/ Paper out !! Excellent work with @asrmoin @dsgoodsell  and @sehnaldavid doi.org/10.1002/pro.5177
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Our second years @AllisonBarkdull, @YutingZhan8328, and @Renhao4 received lab coats this weekend! #computationalscientists #whataretheygonnadowithlabcoats
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congratulations to Ishan for winning second place for his talk at Scripps' Graduate Research Symposium #IshanFold
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Do you know Python and have experience with RDKit? Do you want to work in an exciting and multidisciplinary environment?The AutoDock project is hiring a programmer, apply here! recruiting2.ultipro.com/SCR1…
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A new @nchembio study, led by @_chrisgparker_ alongside Jacob M. Wozniak and Weichao Li, created a high-resolution technique for finding new druggable sites for any human disease, from cancer to Alzheimer’s disease. More at: ow.ly/9NLN50Qnb7x
A protein with unknown binding sites (left), versus a protein showing high-resolution binding site mapping (right). Credit: Scripps Research

ALT A protein with unknown binding sites (left), versus a protein showing high-resolution binding site mapping (right). Credit: Scripps Research

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A new version of Ringtail v1.1, our VS analysis tool, is now available on GitHub (github.com/forlilab/Ringtail) and PyPi (pypi.org/project/ringtail/)! Thanks to the amazing work of Althea, this version is packed with a lot of new features and improvements...
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more replies
Thanks to RDKit, it is possible to filter results by a ligand substructure and its location in space (pharmacophores!) Results can be clustered with Morgan fp and/or interaction fingerprints. Finding ligands with more diverse or similar interactions has never been easier!
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Shout-out to the lab crew that helped with the fearless testing: Matt, @paologoverna, @diogom, @giuliabnc, @popsichen and @manuco17 Grab your free copy and let us know if you like it!
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