Technology and Code

Published on 30 Aug 2021

Models and Processes to Extract Drug-like Molecules From Natural Language Text

in Biological Modeling and Simulation

Zhi Hong
J. Gregory Pauloski
Logan Ward
Kyle Chard
Ben Blaiszik
Ian Foster

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.636077

2,790 views
3 citations

Original Research

Published on 26 Aug 2021

Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors

in Biological Modeling and Simulation

Giuseppe Deganutti
Silvia Atanasio
Roxana-Maria Rujan
Patrick M. Sexton
Denise Wootten
Christopher A. Reynolds

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.720561

4,923 views
6 citations

Original Research

Published on 24 Aug 2021

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin

in Biological Modeling and Simulation

Jules Nde
Pengzhi Zhang
Jacob C. Ezerski
Wei Lu
Kaitlin Knapp
Peter G. Wolynes
Margaret S. Cheung

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.661322

4,799 views
6 citations

Methods

Published on 23 Aug 2021

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

in Biological Modeling and Simulation

Farhan Quadir
Raj S. Roy
Elham Soltanikazemi
Jianlin Cheng

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.716973

12,579 views
21 citations

Original Research

Published on 20 Aug 2021

Packpred: Predicting the Functional Effect of Missense Mutations

in Biological Modeling and Simulation

Kuan Pern Tan
Tejashree Rajaram Kanitkar
Chee Keong Kwoh
Mallur Srivatsan Madhusudhan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.646288

9,066 views
11 citations

Original Research

Published on 20 Aug 2021

Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp

in Biological Modeling and Simulation

Mitul Srivastava
Lovika Mittal
Anita Kumari
Shailendra Asthana

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.639614

4,868 views
18 citations

Original Research

Published on 18 Aug 2021

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks

in Biological Modeling and Simulation

Noelia Ferruz
Florian Michel
Francisco Lobos
Steffen Schmidt
Birte Höcker

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.715972

3,314 views
8 citations

Technology and Code

Published on 18 Aug 2021

SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress

in Biological Modeling and Simulation

Valentín Iglesias
Jaime Santos
Juan Santos-Suárez
Carlos Pintado-Grima
Salvador Ventura

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.718301

3,874 views
12 citations

Technology and Code

Published on 13 Aug 2021

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

in Biological Modeling and Simulation

Genís Bayarri
Adam Hospital
Modesto Orozco

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.726232

4,469 views
8 citations

Original Research

Published on 12 Aug 2021

An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling

in Biological Modeling and Simulation

Kari Gaalswyk
Zhihong Liu
Hans J. Vogel
Justin L. MacCallum

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.676268

3,742 views
5 citations

Methods

Published on 12 Aug 2021

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction

in Biological Modeling and Simulation

Charles Christoffer
Vijay Bharadwaj
Ryan Luu
Daisuke Kihara

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.724947

27,146 views
32 citations

Original Research

Published on 12 Aug 2021

DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

in Biological Modeling and Simulation

Fabrizio Cleri
Marc F. Lensink
Ralf Blossey

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.713003

7,322 views
18 citations

Original Research

Published on 09 Aug 2021

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

in Biological Modeling and Simulation

Łukasz Charzewski
Krystiana A. Krzyśko
Bogdan Lesyng

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.633181

4,384 views
6 citations

Original Research

Published on 06 Aug 2021

Electron Transfer Coupled to Conformational Dynamics in Cell Respiration

in Biological Modeling and Simulation

Marco Reidelbach
Christoph Zimmer
Brigitte Meunier
Peter R. Rich
Vivek Sharma

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.711436

2,609 views
9 citations

Original Research

Published on 06 Aug 2021

Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA

in Biological Modeling and Simulation

Yixin Xie
Chitra B. Karki
Jiawei Chen
Dongfang Liu
Lin Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.718587

3,339 views
8 citations

Original Research

Published on 06 Aug 2021

Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation

in Biological Modeling and Simulation

Yuan-Wei Ma
Tong-You Lin
Min-Yeh Tsai

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.719320

4,018 views
7 citations

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Articles

Models and Processes to Extract Drug-like Molecules From Natural Language Text

Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Packpred: Predicting the Functional Effect of Missense Mutations

Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks

SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction

DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

Electron Transfer Coupled to Conformational Dynamics in Cell Respiration

Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA

Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation