Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

The next decade of protein structure.

Lutomski, Corinne A; El-Baba, Tarick J; Robinson, Carol V; Riek, Roland; Scheres, Sjors H W; Yan, Nieng; AlQuraishi, Mohammed; Gan, Lu.

Cell ; 185(15): 2617-2620, 2022 Jul 21.

Artigo em Inglês | MEDLINE | ID: mdl-35868264

2.

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

Ahdritz, Gustaf; Bouatta, Nazim; Floristean, Christina; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J; Berenberg, Daniel; Fisk, Ian; Zanichelli, Niccolò; Zhang, Bo; Nowaczynski, Arkadiusz; Wang, Bei; Stepniewska-Dziubinska, Marta M; Zhang, Shang; Ojewole, Adegoke; Guney, Murat Efe; Biderman, Stella; Watkins, Andrew M; Ra, Stephen; Lorenzo, Pablo Ribalta; Nivon, Lucas; Weitzner, Brian; Ban, Yih-En Andrew; Chen, Shiyang; Zhang, Minjia; Li, Conglong; Song, Shuaiwen Leon; He, Yuxiong; Sorger, Peter K; Mostaque, Emad; Zhang, Zhao; Bonneau, Richard; AlQuraishi, Mohammed.

Nat Methods ; 2024 May 14.

Artigo em Inglês | MEDLINE | ID: mdl-38744917

3.

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.

AlQuraishi, Mohammed; Sorger, Peter K.

Nat Methods ; 18(10): 1169-1180, 2021 10.

Artigo em Inglês | MEDLINE | ID: mdl-34608321

4.

Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Cunningham, Joseph M; Koytiger, Grigoriy; Sorger, Peter K; AlQuraishi, Mohammed.

Nat Methods ; 17(2): 175-183, 2020 02.

Artigo em Inglês | MEDLINE | ID: mdl-31907444

5.

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.

Liu, Changchang; Kutchukian, Peter; Nguyen, Nhan D; AlQuraishi, Mohammed; Sorger, Peter K.

J Chem Inf Model ; 63(17): 5457-5472, 2023 09 11.

Artigo em Inglês | MEDLINE | ID: mdl-37595065

6.

Unified rational protein engineering with sequence-based deep representation learning.

Alley, Ethan C; Khimulya, Grigory; Biswas, Surojit; AlQuraishi, Mohammed; Church, George M.

Nat Methods ; 16(12): 1315-1322, 2019 12.

Artigo em Inglês | MEDLINE | ID: mdl-31636460

7.

Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin.

Alquraishi, Mohammed; Chahed, Samah; Alani, Dina; Puckett, Dexter L; Dowker, Presley D; Hubbard, Katelin; Zhao, Yi; Kim, Ji Yeon; Nodit, Laurentia; Fatima, Huma; Donohoe, Dallas; Voy, Brynn; Chowanadisai, Winyoo; Bettaieb, Ahmed.

Cell Commun Signal ; 20(1): 76, 2022 05 30.

Artigo em Inglês | MEDLINE | ID: mdl-35637461

8.

Protein-structure prediction revolutionized.

AlQuraishi, Mohammed.

Nature ; 596(7873): 487-488, 2021 08.

Artigo em Inglês | MEDLINE | ID: mdl-34426694

9.

A watershed moment for protein structure prediction.

AlQuraishi, Mohammed.

Nature ; 577(7792): 627-628, 2020 01.

Artigo em Inglês | MEDLINE | ID: mdl-31988401

10.

The Role of PKM2 in Metabolic Reprogramming: Insights into the Regulatory Roles of Non-Coding RNAs.

Puckett, Dexter L; Alquraishi, Mohammed; Chowanadisai, Winyoo; Bettaieb, Ahmed.

Int J Mol Sci ; 22(3)2021 Jan 25.

Artigo em Inglês | MEDLINE | ID: mdl-33503959

11.

AlphaFold at CASP13.

AlQuraishi, Mohammed.

Bioinformatics ; 35(22): 4862-4865, 2019 11 01.

Artigo em Inglês | MEDLINE | ID: mdl-31116374

12.

Zyflamend induces apoptosis in pancreatic cancer cells via modulation of the JNK pathway.

Puckett, Dexter L; Alquraishi, Mohammed; Alani, Dina; Chahed, Samah; Donohoe, Dallas; Voy, Brynn; Whelan, Jay; Bettaieb, Ahmed.

Cell Commun Signal ; 18(1): 126, 2020 08 14.

Artigo em Inglês | MEDLINE | ID: mdl-32795297

13.

ProteinNet: a standardized data set for machine learning of protein structure.

AlQuraishi, Mohammed.

BMC Bioinformatics ; 20(1): 311, 2019 Jun 11.

Artigo em Inglês | MEDLINE | ID: mdl-31185886

14.

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates.

AlQuraishi, Mohammed.

J Comput Chem ; 40(7): 885-892, 2019 03 15.

Artigo em Inglês | MEDLINE | ID: mdl-30614534

15.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide.

BMC Bioinformatics ; 16: 390, 2015 Nov 19.

Artigo em Inglês | MEDLINE | ID: mdl-26586237

16.

Direct inference of protein-DNA interactions using compressed sensing methods.

AlQuraishi, Mohammed; McAdams, Harley H.

Proc Natl Acad Sci U S A ; 108(36): 14819-24, 2011 Sep 06.

Artigo em Inglês | MEDLINE | ID: mdl-21825146

17.

Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens.

Walsh, Zachary H; Shah, Parin; Kothapalli, Neeharika; Shah, Shivem B; Nikolenyi, Gergo; Brodtman, D Zack; Leuzzi, Giuseppe; Rogava, Meri; Mu, Michael; Ho, Patricia; Abuzaid, Sinan; Vasan, Neil; AlQuraishi, Mohammed; Milner, Joshua D; Ciccia, Alberto; Melms, Johannes C; Izar, Benjamin.

Nat Biotechnol ; 2024 May 23.

Artigo em Inglês | MEDLINE | ID: mdl-38783148

18.

Three enhancements to the inference of statistical protein-DNA potentials.

AlQuraishi, Mohammed; McAdams, Harley H.

Proteins ; 81(3): 426-42, 2013 Mar.

Artigo em Inglês | MEDLINE | ID: mdl-23042633

19.

High-throughput deep learning variant effect prediction with Sequence UNET.

Dunham, Alistair S; Beltrao, Pedro; AlQuraishi, Mohammed.

Genome Biol ; 24(1): 110, 2023 05 09.

Artigo em Inglês | MEDLINE | ID: mdl-37161576

20.

Growing ecosystem of deep learning methods for modeling protein-protein interactions.

Rogers, Julia R; Nikolényi, Gergo; AlQuraishi, Mohammed.

Protein Eng Des Sel ; 362023 Jan 21.

Artigo em Inglês | MEDLINE | ID: mdl-38102755

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The next decade of protein structure.

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.

Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.

Unified rational protein engineering with sequence-based deep representation learning.

Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin.

Protein-structure prediction revolutionized.

A watershed moment for protein structure prediction.

The Role of PKM2 in Metabolic Reprogramming: Insights into the Regulatory Roles of Non-Coding RNAs.

AlphaFold at CASP13.

Zyflamend induces apoptosis in pancreatic cancer cells via modulation of the JNK pathway.

ProteinNet: a standardized data set for machine learning of protein structure.

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

Direct inference of protein-DNA interactions using compressed sensing methods.

Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens.

Three enhancements to the inference of statistical protein-DNA potentials.

High-throughput deep learning variant effect prediction with Sequence UNET.

Growing ecosystem of deep learning methods for modeling protein-protein interactions.