Literature DB >> 34423314

Biomolecular modeling thrives in the age of technology.

Tamar Schlick1,2,3, Stephanie Portillo-Ledesma1.   

Abstract

The biomolecular modeling field has flourished since its early days in the 1970s due to the rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase in size and timespan of biomolecular simulations has outpaced Moore's law. Here, we discuss the role of knowledge-based versus physics-based methods and hardware versus software advances in propelling the field forward. This rapid adaptation and outreach suggests a bright future for modeling, where theory, experimentation and simulation define three pillars needed to address future scientific and biomedical challenges.

Entities:  

Year:  2021        PMID: 34423314      PMCID: PMC8378674          DOI: 10.1038/s43588-021-00060-9

Source DB:  PubMed          Journal:  Nat Comput Sci        ISSN: 2662-8457


  127 in total

Review 1.  Biomolecular simulation: a computational microscope for molecular biology.

Authors:  Ron O Dror; Robert M Dirks; J P Grossman; Huafeng Xu; David E Shaw
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

2.  Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub.

Authors:  Gavin D Bascom; Christopher G Myers; Tamar Schlick
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-04       Impact factor: 11.205

3.  'It will change everything': DeepMind's AI makes gigantic leap in solving protein structures.

Authors:  Ewen Callaway
Journal:  Nature       Date:  2020-12       Impact factor: 49.962

4.  High-accuracy protein structures by combining machine-learning with physics-based refinement.

Authors:  Lim Heo; Michael Feig
Journal:  Proteins       Date:  2019-11-15

5.  Targeted Adversarial Learning Optimized Sampling.

Authors:  Jun Zhang; Yi Isaac Yang; Frank Noé
Journal:  J Phys Chem Lett       Date:  2019-09-18       Impact factor: 6.475

6.  Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

Authors:  Jaewoon Jung; Wataru Nishima; Marcus Daniels; Gavin Bascom; Chigusa Kobayashi; Adetokunbo Adedoyin; Michael Wall; Anna Lappala; Dominic Phillips; William Fischer; Chang-Shung Tung; Tamar Schlick; Yuji Sugita; Karissa Y Sanbonmatsu
Journal:  J Comput Chem       Date:  2019-04-17       Impact factor: 3.376

7.  Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

Authors:  Alpan Raval; Stefano Piana; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  Proteins       Date:  2012-05-15

8.  Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

Authors:  Hahnbeom Park; Gyu Rie Lee; Lim Heo; Chaok Seok
Journal:  PLoS One       Date:  2014-11-24       Impact factor: 3.240

9.  Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism.

Authors:  Jacob D Durrant; Sarah E Kochanek; Lorenzo Casalino; Pek U Ieong; Abigail C Dommer; Rommie E Amaro
Journal:  ACS Cent Sci       Date:  2020-02-19       Impact factor: 14.553

10.  Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.

Authors:  Sergey Ovchinnikov; David E Kim; Ray Yu-Ruei Wang; Yuan Liu; Frank DiMaio; David Baker
Journal:  Proteins       Date:  2016-02-24
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  9 in total

1.  rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.

Authors:  Ya-Lan Tan; Xunxun Wang; Ya-Zhou Shi; Wenbing Zhang; Zhi-Jie Tan
Journal:  Biophys J       Date:  2021-11-17       Impact factor: 4.033

2.  Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function.

Authors:  Manoj Thakur; Rishikesh S Parulekar; Sagar S Barale; Kailas D Sonawane; Kalappa Muniyappa
Journal:  Biophys J       Date:  2022-07-09       Impact factor: 3.699

3.  BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations.

Authors:  Genís Bayarri; Pau Andrio; Adam Hospital; Modesto Orozco; Josep Lluís Gelpí
Journal:  Nucleic Acids Res       Date:  2022-05-26       Impact factor: 19.160

4.  Unraveling membrane properties at the organelle-level with LipidDyn.

Authors:  Simone Scrima; Matteo Tiberti; Alessia Campo; Elisabeth Corcelle-Termeau; Delphine Judith; Mads Møller Foged; Knut Kristoffer Bundgaard Clemmensen; Sharon A Tooze; Marja Jäättelä; Kenji Maeda; Matteo Lambrughi; Elena Papaleo
Journal:  Comput Struct Biotechnol J       Date:  2022-06-30       Impact factor: 6.155

5.  Molecular Paradigms for Biological Mechanosensing.

Authors:  David Gomez; Willmor J Peña Ccoa; Yuvraj Singh; Enrique Rojas; Glen M Hocky
Journal:  J Phys Chem B       Date:  2021-10-28       Impact factor: 3.466

6.  Finite element modeling of α-helices and tropocollagen molecules referring to spike of SARS-CoV-2.

Authors:  Tomasz Wierzbicki; Yuanli Bai
Journal:  Biophys J       Date:  2022-05-20       Impact factor: 3.699

7.  A MULTISCALE VISION-ILLUSTRATIVE APPLICATIONS FROM BIOLOGY TO ENGINEERING.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma; Mischa Blaszczyk; Luke Dalessandro; Somnath Ghosh; Klaus Hackl; Cale Harnish; Shravan Kotha; Daniel Livescu; Arif Masud; Karel Matouš; Arturo Moyeda; Caglar Oskay; Jacob Fish
Journal:  Int J Multiscale Comput Eng       Date:  2021       Impact factor: 1.508

Review 8.  Pharmacoproteomics of Brain Barrier Transporters and Substrate Design for the Brain Targeted Drug Delivery.

Authors:  Kristiina M Huttunen; Tetsuya Terasaki; Arto Urtti; Ahmed B Montaser; Yasuo Uchida
Journal:  Pharm Res       Date:  2022-03-07       Impact factor: 4.580

9.  Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.

Authors:  Daiki Matsubara; Kento Kasahara; Hisham M Dokainish; Hiraku Oshima; Yuji Sugita
Journal:  Molecules       Date:  2022-09-05       Impact factor: 4.927

  9 in total

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