Flexible protein –protein docking with a multitrack iterative transformer
AbstractConventional protein –protein docking algorithms usually rely on heavy candidate sampling and reranking, but these steps are time-consuming and hinder applications that require high-throughput complex structure prediction, for example, structure-based virtual screening. Existing deep learning methods for protein–pro tein docking, despite being much faster, suffer from low docking success rates. In addition, they simplify the problem to assume no conformational changes within any protein upon binding (rigid docking). This assumption precludes applications when binding-induced conformational changes play a role, ...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Lee ‐Shin Chu,
Jeffrey A. Ruffolo,
Ameya Harmalkar,
Jeffrey J. Gray Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
Cover Image
In addition to known proteins such as ACE2, other extracellular cell surface proteins may bind with the SARS-CoV-2 spike protein, potentially playing a role in viral entry into the host cell. Computational and surface plasmon resonance results show that perlecan LG3 stably binds with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein at a site different from the ACE2-binding interface. Shown here is the LG3 (red)-RBD (gray)-ACE2 (blue) complex obtained by molecular docking and simulations. For details, see: Gressett and Hossen et al.,Protein Science, 2023.https://doi.org/10.1002/pro.4843 (Source: Protein Science)
Source: Protein Science - January 22, 2024 Category: Biochemistry Tags: Cover Image Source Type: research
Issue information
(Source: Protein Science)
Source: Protein Science - January 22, 2024 Category: Biochemistry Tags: Issue Information Source Type: research
PBITV3: A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - January 4, 2024 Category: Biochemistry Authors: Shuvechha Chakraborty,
Mehdi Askari,
Ram Shankar Barai,
Susan Idicula ‐Thomas Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP ‐43 and modulates its phase behavior
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - January 1, 2024 Category: Biochemistry Authors: Priyesh Mohanty,
Azamat Rizuan,
Young C. Kim,
Nicolas L. Fawzi,
Jeetain Mittal Tags: RESEARCH ARTICLE Source Type: research
Structural characterization of the Sel1 ‐like repeat protein LceB from Legionella pneumophila
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 31, 2023 Category: Biochemistry Authors: Tiffany V. Penner,
Neil Lorente Cobo,
Deepak T. Patel,
Dhruvin H. Patel,
Alexei Savchenko,
Ann Karen C. Brassinga,
Gerd Prehna Tags: RESEARCH ARTICLE Source Type: research
Functional Production and Biochemical Investigation of an Integral Membrane Enzyme for Olefin Biosynthesis
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 31, 2023 Category: Biochemistry Authors: Subhashini Murugan,
Tabish Iqbal,
Debasis Das Tags: RESEARCH ARTICLE Source Type: research
The mineralocorticoid receptor forms higher order oligomers upon DNA binding
AbstractThe prevailing model of steroid hormone nuclear receptor function assumes ligand-induced homodimer formation followed by binding to DNA hormone response elements (HREs). This model has been challenged by evidence showing that the glucocorticoid receptor (GR) forms tetramers upon ligand and DNA binding, which then drive receptor-mediated gene transactivation and transrepression. GR and the closely-related mineralocorticoid receptors (MR) interact to transduce corticosteroid hormone signaling, but whether they share the same quaternary arrangement is unknown. Here, we used a fluorescence imaging technique, Number& Br...
Source: Protein Science - December 31, 2023 Category: Biochemistry Authors: Gregory Fettweis,
Thomas A. Johnson,
Brian Almeida ‐Prieto,
Julián Weller‐Pérez,
Diego M. Presman,
Gordon L. Hager,
Diego Alvarez de la Rosa Tags: RESEARCH ARTICLE Source Type: research
Crystal structure of human serum albumin in complex with megabody reveals unique human and murine cross ‐reactive binding site
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 28, 2023 Category: Biochemistry Authors: Sofia De Felice,
Zhanna Romanyuk,
Monica Chinellato,
Giulia Zoia,
Sara Linciano,
Yoichi Kumada,
Els Pardon,
Jan Steyaert,
Alessandro Angelini,
Laura Cendron Tags: RESEARCH NOTE Source Type: research
Investigating Lysozyme Amyloid Fibril Formation and Structural Variability Dependence on its Initial Folding State Under Different pH Conditions
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 28, 2023 Category: Biochemistry Authors: Mantas Ziaunys,
Kamile Mikalauskaite,
Andrius Sakalauskas,
Vytautas Smirnovas Tags: RESEARCH ARTICLE Source Type: research
Helicobacter pylori FlgN binds its substrate FlgK and the Flagellum ATPase FliI in a similar manner observed for the FliT chaperone
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 28, 2023 Category: Biochemistry Authors: Poonam Dhindwal,
Michal T. Boniecki,
Stanley A. Moore Tags: RESEARCH ARTICLE Source Type: research
Engineering Highly Stable Variants of Corynactis Californica Green Fluorescent Proteins
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 28, 2023 Category: Biochemistry Authors: Li ‐Wei Hung,
Thomas C. Terwilliger,
Geoffrey S. Waldo,
Hau B. Nguyen Tags: RESEARCH ARTICLE Source Type: research
Dimerization of the CNNM extracellular domain
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 27, 2023 Category: Biochemistry Authors: Ashkan Shahsavan,
Emma L. Lee,
Katalin Illes,
Guennadi Kozlov,
Kalle Gehring Tags: RESEARCH NOTE Source Type: research
Flexible Protein ‐Protein Docking with a Multi‐Track Iterative Transformer
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - December 27, 2023 Category: Biochemistry Authors: Lee ‐Shin Chu,
Jeffrey A. Ruffolo,
Ameya Harmalkar,
Jeffrey J. Gray Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
FRAGSITE2: A structure and fragment ‐based approach for virtual ligand screening
AbstractProtein function annotation and drug discovery often involve finding small molecule binders. In the early stages of drug discovery, virtual ligand screening (VLS) is frequently applied to identify possible hits before experimental testing. While our recent ligand homology modeling (LHM)-machine learning VLS method FRAGSITE outperformed approaches that combined traditional docking to generate protein –ligand poses and deep learning scoring functions to rank ligands, a more robust approach that could identify a more diverse set of binding ligands is needed. Here, we describe FRAGSITE2 that shows significant improve...
Source: Protein Science - December 27, 2023 Category: Biochemistry Authors: Hongyi Zhou,
Jeffrey Skolnick Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
