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Sampling alternative conformational states of transporters and receptors with AlphaFold2

eLife, 2022-03, Vol.11

2022

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Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007597-e1007597

2020

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Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

PloS one, 2015-07, Vol.10 (7), p.e0132508-e0132508

2015

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Prediction of amphipathic helix-membrane interactions with Rosetta

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008818

2021

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Assessing multiple score functions in Rosetta for drug discovery

PloS one, 2020-10, Vol.15 (10), p.e0240450-e0240450

2020

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Towards ligand docking including explicit interface water molecules

PloS one, 2013-06, Vol.8 (6), p.e67536-e67536

2013

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Potently neutralizing and protective human antibodies against SARS-CoV-2

Nature (London), 2020-08, Vol.584 (7821), p.443-449

2020

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Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders

Nature reviews. Drug discovery, 2014-09, Vol.13 (9), p.692-708

2014

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Docking cholesterol to integral membrane proteins with Rosetta

PLoS computational biology, 2023-03, Vol.19 (3), p.e1010947-e1010947

2023

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Structure of a Class C GPCR Metabotropic Glutamate Receptor 1 Bound to an Allosteric Modulator

Science (American Association for the Advancement of Science), 2014-04, Vol.344 (6179), p.58-64

2014

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PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking

PloS one, 2022-05, Vol.17 (5), p.e0269072-e0269072

2022

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Rosetta design with co-evolutionary information retains protein function

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008568-e1008568

2021

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Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection

International journal of molecular sciences, 2023-04, Vol.24 (9), p.7788

2023

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Pharmacological evaluation of new constituents of “Spice”: synthetic cannabinoids based on indole, indazole, benzimidazole and carbazole scaffolds

Forensic toxicology, 2018-07, Vol.36 (2), p.385-403

2018

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Structure–function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting

Nature communications, 2021-03, Vol.12 (1), p.1382-15, Article 1382

2021

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An Investigation of Three-Finger Toxin-nAChR Interactions through Rosetta Protein Docking

Toxins, 2020-09, Vol.12 (9), p.598

2020

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Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants

PloS one, 2024-01, Vol.19 (1), p.e0297560

2024

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On-target Resistance to the Mutant-Selective EGFR Inhibitor Osimertinib Can Develop in an Allele-Specific Manner Dependent on the Original EGFR-Activating Mutation

Clinical cancer research, 2019-06, Vol.25 (11), p.3341-3351

2019

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Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2

Biophysical journal, 2023-06, Vol.122 (11), p.2041-2052

2023

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Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids

PloS one, 2022-12, Vol.17 (12), p.e0275759

2022

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Discovery of Small-Molecule Modulators of the Human Y4 Receptor

PloS one, 2016-06, Vol.11 (6), p.e0157146-e0157146

2016

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Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010230-e1010230

2022

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The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors

Nature chemical biology, 2018-03, Vol.14 (3), p.284-290

2018

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BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

Journal of cheminformatics, 2015-09, Vol.7 (1), p.47-47, Article 47

2015

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Conformational Flexibility and Structural Dynamics in GPCR-Mediated G Protein Activation: A Perspective

Journal of molecular biology, 2013-07, Vol.425 (13), p.2288-2298

2013

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Sampling alternative conformational states of transporters and receptors with AlphaFold2

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

Prediction of amphipathic helix-membrane interactions with Rosetta

Assessing multiple score functions in Rosetta for drug discovery

Towards ligand docking including explicit interface water molecules

Potently neutralizing and protective human antibodies against SARS-CoV-2

Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders

Docking cholesterol to integral membrane proteins with Rosetta

Structure of a Class C GPCR Metabotropic Glutamate Receptor 1 Bound to an Allosteric Modulator

PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking

Rosetta design with co-evolutionary information retains protein function

Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection

Pharmacological evaluation of new constituents of “Spice”: synthetic cannabinoids based on indole, indazole, benzimidazole and carbazole scaffolds

Structure–function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting

An Investigation of Three-Finger Toxin-nAChR Interactions through Rosetta Protein Docking

Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants

On-target Resistance to the Mutant-Selective EGFR Inhibitor Osimertinib Can Develop in an Allele-Specific Manner Dependent on the Original EGFR-Activating Mutation

Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2

Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids

Discovery of Small-Molecule Modulators of the Human Y4 Receptor

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods

The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors

BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

Conformational Flexibility and Structural Dynamics in GPCR-Mediated G Protein Activation: A Perspective

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