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Theoretical and Computational Chemistry

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How good are AlphaFold models for docking-based virtual screening?

Valeria Scardino, Juan I. Di Filippo, Claudio Cavasotto

Version 1 posted 06 September 2022

1,511

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3

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Biological and Medicinal Chemistry

Working Paper

PINNED: Identifying Characteristics of Druggable Human Proteins Using an Interpretable Neural Network

Michael Cunningham, Danielle Pins, Zoltan Dezso, Maricel Torrent, Aparna Vasanthakumar, Abhishek Pandey

Version 1 posted 30 March 2023

318

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Theoretical and Computational Chemistry

Working Paper

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Yuqi Zhang, Marton Vass, Da Shi, Esam Abualrous, Jenny Chambers, Nikita Chopra, Chris Higgs, Koushik Kasavajhala, Hubert Li, Prajwal Nandekar, Hideyuki Sato, Edward Miller, Matt Repasky, Steven Jerome

Version 2 posted 27 June 2022

2,903

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4

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Theoretical and Computational Chemistry

Working Paper

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Dilek Coskun, Muyun Lihan, Joao Rodrigues, Marton Vass, Daniel Robinson, Richard Friesner, Edward Miller

Version 3 posted 03 August 2023

1,571

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Biological and Medicinal Chemistry

Working Paper

Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti-neuroblastoma Activity

Fady Baselious, Sebastian Hilscher, Sven Hagemann, Sunita Tripathee, Dina Robaa, Cyril Barinka, Stefan Hüttelmaier, Mike Schutkowski, Wolfgang Sippl

Version 1 posted 09 January 2024

340

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Theoretical and Computational Chemistry

Working Paper

Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3

Francisco Erazo, Nils Dunlop, Farzaneh Jalalypour, Rocío Mercado

Version 1 posted 06 March 2025

556

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Theoretical and Computational Chemistry

Working Paper

A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors

Hirotada Kaneshiro, Masakazu Sato, Airi Tanaka, Shuya Nakata, Yoshiko Aihara, Hirotaka Kitoh-Nishioka, Yoshiharu Mori, Shigenori Tanaka

Version 1 posted 19 May 2025

27

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Biological and Medicinal Chemistry

Working Paper

dMSGB-IE: Computational Mutational Scanning for (de)Methylation Thermodynamics

Zhendong Li, Lei Zheng, Yuqing Yang, Xiaohui Wang, Zhaoxi Sun, John Zeng Hui Zhang

Version 1 posted 21 January 2025

157

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Biological and Medicinal Chemistry

Working Paper

HSADab2025: AI-powered Modelling of Human Serum Albumin

Lei Zheng, Xiaohui Wang, Xiao Liu, Mao Wang, John Zeng Hui Zhang, Zuo-yuan Zhang, Zhaoxi Sun

Version 1 posted 10 January 2025

270

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Theoretical and Computational Chemistry

Working Paper

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy

Sudarshan Behera, David Hahn, Carter Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert de Groot

Version 2 posted 28 April 2025

273

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Refine Search

11 results in alphafold in Keywords: alphafold

How good are AlphaFold models for docking-based virtual screening?

PINNED: Identifying Characteristics of Druggable Human Proteins Using an Interpretable Neural Network

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti-neuroblastoma Activity

Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3

A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors

dMSGB-IE: Computational Mutational Scanning for (de)Methylation Thermodynamics

HSADab2025: AI-powered Modelling of Human Serum Albumin

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy

11 results in Keywords: alphafold