Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Patrick Bryant
The structural history of Eukarya
Reference #1 Abstract INTRODUCTION RESULTS DISCUSSION MATERIALS AND METHODS Acknowledgments Supplementary Materials REFERENCES eLetters (0) Information & Authors Metrics & Citations View Options References Figures Tables Media Share This article has 0 eLetter . Abstract Comparative genomics has traditionally relied on sequence-based markers, yet the global evolutionary landscape of protein architecture remains largely unexplored.
Correlation of Norovirus in Wastewater with Gastroenteritis-Related Hospitalizations, New York, USA, 2022-2024
Noroviruses are genetically diverse icosahedral viruses belonging to the family Caliciviridae; they consist of a single-stranded, positive-sense RNA genome. They are a leading cause of diarrheal disease. and can infect a wide variety of hosts (1). Norovirus consists of 10 genogroups (GI–GX) and 49 genotypes. Genogroups GI, GII, GIV, GVIII and GIX are known to infect humans, whereas genogroup GIII primarily infects cows and GV mice (1–4).
Design of linear and cyclic peptide binders from protein sequence information - Communications Chemistry
Abstract Structure prediction technology has transformed protein design, yet key challenges remain, particularly in designing novel functions. Many proteins function through interactions with other proteins, making the rational design of these interactions a central problem. While most efforts focus on large, stable proteins, shorter peptides offer advantages such as lower manufacturing costs, reduced steric hindrance, and improved cell permeability when cyclised.
AI-first structural identification of pathogenic protein target interfaces
Loading metrics Open Access Peer-reviewed Research Article ? This is an uncorrected proof. Citation: Saluri M, Landreh M, Bryant P (2025) AI-first structural identification of pathogenic protein target interfaces. PLoS Comput Biol 21(6): e1013168. https://doi.org/10.1371/journal.pcbi.1013168 Editor: Jeffrey Skolnick, Georgia Institute of Technology, UNITED STATES OF AMERICA Received: March 11, 2025; Accepted: May 26, 2025; Published: June 26, 2025 Copyright: © 2025 Saluri et al.
Design of linear and cyclic peptide binders of different lengths from protein sequence information
Abstract Structure prediction technology has revolutionised the field of protein design, but key questions such as how to design new functions remain. Many proteins exert their functions through interactions with other proteins, and a significant challenge is designing these interactions effectively.
Structure prediction of alternative protein conformations - Nature Communications
Abstract Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB. However, almost all protein structures with multiple conformations represented in the PDB have been used while training these models.
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Loading metrics Open Access Peer-reviewed Research Article ? This is an uncorrected proof. Citation: Bryant P, Noé F (2024) Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile. PLoS Comput Biol 20(7): e1012253. https://doi.org/10.1371/journal.pcbi.1012253 Editor: Dina Schneidman, Hebrew University of Jerusalem, ISRAEL Received: October 20, 2023; Accepted: June 14, 2024; Published: July 25, 2024 Copyright: © 2024 Bryant, Noé.
Design of linear and cyclic peptide binders of different lengths only from a protein target sequence
Abstract Structure prediction technology has revolutionised the field of protein design, but key questions such as how to design new functions remain. Many proteins exert their functions through interactions with other proteins, and a significant challenge is designing these interactions effectively.
Structure prediction of protein-ligand complexes from sequence information with Umol - Nature Communications
Abstract Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly from sequence information.
Structure prediction of protein-ligand complexes from sequence information with Umol
Abstract Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly, given a multiple sequence alignment representation of the protein and a SMILES string representing the ligand.
Peptide binder design with inverse folding and protein structure prediction - Communications Chemistry
Abstract The computational design of peptide binders towards a specific protein interface can aid diagnostic and therapeutic efforts. Here, we design peptide binders by combining the known structural space searched with Foldseek, the protein design method ESM-IF1, and AlphaFold2 (AF) in a joint framework. Foldseek generates backbone seeds for a modified version of ESM-IF1 adapted to protein complexes.
Structure prediction of alternative protein conformations
Abstract Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins in the conformations most likely to exist in the PDB. However, almost all conformations in the PDB are seen during training. Therefore, it is not possible to assess whether alternative protein conformations can be predicted or if these are reproduced from memory.
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
IJMS | Free Full-Text | A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
Open AccessArticle by Elin Barnekow 1,2,*, Johan Hasslow 2, Wen Liu 3,4, Patrick Bryant 3,5,6, Jessada Thutkawkorapin 3, Camilla Wendt 1,2, Kamila Czene 7, Per Hall 2,7, Sara Margolin 1,2 and Annika Lindblom 3,8,* 1 Department of Clinical Science and Education, Karolinska Institutet, 11883 Stockholm, Sweden 2 Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden 3 Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden 4 Department of...
Towards a structurally resolved human protein interaction network - Nature Structural & Molecular Biology
Protein interaction data and annotations Human protein pairs known to physically interact were obtained from the hu.MAP dataset, retaining pairwise protein interactions with ≥0.5 confidence, and most interactions from the HuRI dataset. These interactions were further enriched by obtaining annotations on crosslinked peptides matched across pairs of interaction proteins, disease-related mutations and protein phosphorylation sites in the selected proteins.
A structural biology community assessment of AlphaFold2 applications - Nature Structural & Molecular Biology
|
Abstract Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested.
By Arthur O. Zalevsky, Patrick Bryant, Lydia L. Good, Roman A. Laskowski, Gabriele Pozzati, Aditi Shenoy, Victoria Ruiz Serra, Alistair S. Dunham, David Burke, Sameer Velankar, Adam Frost, Kresten Lindorff-Larsen, Alex Bateman, Andrey V. Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David Ascher, Janet Thornton, Norman E. Davey, Amelie Stein, Arne Elofsson, Tristan I. Croll
|
Nature
Verified
Towards a structurally resolved human protein interaction network
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
EvoBind: in silico directed evolution of peptide binders with AlphaFold
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Predicting the structure of large protein complexes using AlphaFold and sequential assembly
Abstract AlphaFold and AlphaFold-multimer can predict the structure of single- and multiple chain proteins with very high accuracy. However, predicting protein complexes with more than a handful of chains is still unfeasible, as the accuracy rapidly decreases with the number of chains and the protein size is limited by the memory on a GPU. Nevertheless, it might be possible to predict the structure of large complexes starting from predictions of subcomponents.
Improved prediction of protein-protein interactions using AlphaFold2
Abstract Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes.
Towards a structurally resolved human protein interaction network
New Results View ORCID ProfileDavid F Burke, View ORCID ProfilePatrick Bryant, View ORCID ProfileInigo Barrio-Hernandez, View ORCID ProfileDanish Memon, View ORCID ProfileGabriele Pozzati, Aditi Shenoy, Wensi Zhu, View ORCID ProfileAlistair S Dunham, Pascal Albanese, Andrew Keller, Richard A Scheltema, James B Bruce, Alexander Leitner, View ORCID ProfilePetras Kundrotas, View ORCID ProfilePedro Beltrao, View ORCID ProfileArne Elofsson doi: https://doi.org/10.1101/2021.11.08.467664 Abstract...
Avondale Estates City Manager: Beer scene makes city great place to live, work and play
Editor’s note: Avondale City Manager Patrick Bryant produces a monthly column about local issues. Decaturish offered to republish his columns here to help keep our readers apprised of all things Avondale.
Phoenix Razing: 9 Buildings That Deserve Demolition
Local preservationists are still clutching their stomachs and groaning about our latest architectural loss. In late February, the Molly Helen Neal house at 120 East Willetta Street was bulldozed by developers who recently bought the property. Built in 1920 and designed by famed architectural firm Lescher and Mahoney, the building was offered for free to anyone who could pay to move it.
Curious Nature Hosts Jackalope Taxidermy Workshop
Or sign in with a social account: FACEBOOK GOOGLE + YAHOO! Connect. Discover. Share. Get the most out of your experience with a personalized all-access pass to everything local on events, music, restaurants, news and more. Enter your email or sign up with a social account to get started FACEBOOK TWITTER GOOGLE+ YAHOO!
Students Lead the Way as 15,000 March for Our Lives in Phoenix
Fifteen thousand students and their supporters from all over Arizona rallied on Saturday, March 24, at the State Capitol, joining their peers in a nationwide event to demand their lawmakers take action on guns. Following the lead of the Parkland, Florida, school shooting survivors, Phoenix high schoolers organized a March for Our Lives protest to demand an end to gun violence, as did their contemporaries in dozens of cities around the country.
Record number of competitors dance for the title at 2018 World Championship Hoop Dance Contest
Or sign in with a social account: FACEBOOK GOOGLE + YAHOO! Connect. Discover. Share. Get the most out of your experience with a personalized all-access pass to everything local on events, music, restaurants, news and more. Enter your email or sign up with a social account to get started FACEBOOK TWITTER GOOGLE+ YAHOO!
Talladega City Manager Patrick Bryant addresses state of city (opinion)
Editor’s note: Patrick Bryant has been Talladega city manager since 2015. In conjunction with the unveiling of the municipality’s new logo and slogan Thursday night, he shared some thoughts about the state of the city and the rebranding effort.We have accomplished a lot over the past year.Citizens Baptist announced a merger with Tenet Health and formed the Brookwood Baptist Health System.
A message from Talladega City Manager Patrick Bryant
Thanks to your help, our police department was able to apprehend the suspects involved in both of our recent homicides. I know crime and safety is a great concern of yours, and I will do everything in my power to ensure all Talladega residents have a safe community in which to live, work and play.
Why Do Therapists Charge So Much?
The world can be a stressful place. You are feeling overwhelmed, and nothing seems to be working consistently. You’ve reached out to friends and family. They may have helped a little, but not enough. Perhaps friends or family are somehow associated with your stress, which leaves fewer people in whom to confide. The day has come when you finally decide to seek help to get where you want to be.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Patrick
Contact Patrick, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack