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Molecular dynamics

The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics

John H. Dupuis, Shenlin Wang, Chen Song, Rickey Y. Yada

published 25 Aug 2020

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Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors

Rydberg Roman Supo-Escalante, Aldhair Médico, Eduardo Gushiken, Gustavo E. Olivos-Ramírez, Yaneth Quispe, Fiorella Torres, Melissa Zamudio, Ricardo Antiparra, L. Mario Amzel, Robert H. Gilman, Patricia Sheen, Mirko Zimic

published 31 Jul 2020

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In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation

M. Iqbal Choudhary, Muniza Shaikh, Atia- tul-Wahab, Atta- ur-Rahman

published 24 Jul 2020

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PLD2–PI(4,5)P2 interactions in fluid phase membranes: Structural modeling and molecular dynamics simulations

Kyungreem Han, Richard W. Pastor, Cristina Fenollar–Ferrer

published 20 Jul 2020

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Docking studies and molecular dynamics simulations of the binding characteristics of waldiomycin and its methyl ester analog to Staphylococcus aureus histidine kinase

Awwad Radwan, Gamal M. Mahrous

published 05 Jun 2020

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Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA

Pedro Túlio Resende-Lara, David Perahia, Ana Lígia Scott, Antônio Sérgio Kimus Braz

published 04 Jun 2020

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Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S. Wylie, Wenze Gu, Jessie Huang, F. Marty Ytreberg, Mandar T. Naik, Daniel M. Weinreich, Brenda M. Rubenstein

published 29 May 2020

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Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability

Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele

published 13 May 2020

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Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding

Rumbidzai Chitongo, Adetayo Emmanuel Obasa, Sello Given Mikasi, Graeme Brendon Jacobs, Ruben Cloete

published 07 May 2020

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Effect of linker on the binding free energy of stapled p53/HDM2 complex

Haeri Im, Sihyun Ham

published 30 Apr 2020

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Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

Kai Pua, Daisuke Yuhara, Sho Ayuba, Kenji Yasuoka

published 21 Apr 2020

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Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics

Philip Horx, Armin Geyer

published 13 Apr 2020

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Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach

Nematollah Gheibi, Mohamad Ghorbani, Hanifeh Shariatifar, Alireza Farasat

published 26 Mar 2020

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