Molecular dynamics study of enhanced Man5B enzymatic activity

Autor Bernardi, Rafael C, Cann, Isaac, Schulten, Klaus
Vydáno 2014

Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

Autor Bernardi, Rafael C., Melo, Marcelo C. R., Schulten, Klaus
Vydáno v Biochim Biophys Acta (2014)

Molecular mechanism of extreme mechanostability in a pathogen adhesin

Autor Milles, Lukas F., Bernardi, Rafael C., Schulten, Klaus, Gaub, Hermann E.
Vydáno v Science (2018)

Streptavidin/biotin: Tethering geometry defines unbinding mechanics

Autor Sedlak, Steffen M., Schendel, Leonard C., Gaub, Hermann E., Bernardi, Rafael C.
Vydáno v Sci Adv (2020)

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Autor Scheurer, Maximilian, Rodenkirch, Peter, Siggel, Marc, Bernardi, Rafael C., Schulten, Klaus, Tajkhorshid, Emad, Rudack, Till
Vydáno v Biophys J (2018)

Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A

Autor Haataja, Tatu J.K., Bernardi, Rafael C., Lecointe, Simon, Capoulade, Romain, Merot, Jean, Pentikäinen, Ulla
Vydáno v Structure (2018)

High force catch bond mechanism of bacterial adhesion in the human gut

Autor Liu, Zhaowei, Liu, Haipei, Vera, Andrés M., Bernardi, Rafael C., Tinnefeld, Philip, Nash, Michael A.
Vydáno v Nat Commun (2020)

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

Autor Verdorfer, Tobias, Bernardi, Rafael C, Meinhold, Aylin, Ott, Wolfgang, Luthey-Schulten, Zaida, Nash, Michael A, Gaub, Hermann E
Vydáno v J Am Chem Soc (2017)

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

Autor Ribeiro, João V., Bernardi, Rafael C., Rudack, Till, Stone, John E., Phillips, James C., Freddolino, Peter L., Schulten, Klaus
Vydáno v Sci Rep (2016)

Skeletal Dysplasia Mutations Effect on Human Filamins’ Structure and Mechanosensing

Autor Seppälä, Jonne, Bernardi, Rafael C., Haataja, Tatu J. K., Hellman, Maarit, Pentikäinen, Olli T., Schulten, Klaus, Permi, Perttu, Ylänne, Jari, Pentikäinen, Ulla
Vydáno v Sci Rep (2017)

COMPUTATIONAL METHODOLOGIES for REAL-SPACE STRUCTURAL REFINEMENT of LARGE MACROMOLECULAR COMPLEXES

Autor Goh, Boon Chong, Hadden, Jodi A., Bernardi, Rafael C., Singharoy, Abhishek, McGreevy, Ryan, Rudack, Till, Cassidy, C. Keith, Schulten, Klaus
Vydáno v Annu Rev Biophys (2016)

Molecular dynamics simulations of large macromolecular complexes

Autor Perilla, Juan R., Goh, Boon Chong, Cassidy, C. Keith, Liu, Bo, Bernardi, Rafael C., Rudack, Till, Yu, Hang, Wu, Zhe, Schulten, Klaus
Vydáno v Curr Opin Struct Biol (2015)

Direction Matters – Monovalent Streptavidin:Biotin Complex under Load

Autor Sedlak, Steffen M., Schendel, Leonard C., Melo, Marcelo C. R., Pippig, Diana A., Luthey-Schulten, Zaida, Gaub, Hermann E., Bernardi, Rafael C.
Vydáno v Nano Lett (2018)

Mapping mechanical force propagation through biomolecular complexes

Autor Schoeler, Constantin, Bernardi, Rafael C., Malinowska, Klara H., Durner, Ellis, Ott, Wolfgang, Bayer, Edward A., Schulten, Klaus, Nash, Michael A., Gaub, Hermann E.
Vydáno v Nano Lett (2015)

Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy

Autor Bernardi, Rafael C., Durner, Ellis, Schoeler, Constantin, Malinowska, Klara H., Carvalho, Bruna G., Bayer, Edward A., Luthey-Schulten, Zaida, Gaub, Hermann E., Nash, Michael A.
Vydáno v J Am Chem Soc (2019)

Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products

Autor Cann, Isaac, Pereira, Gabriel V., Abdel-Hamid, Ahmed M., Kim, Heejin, Wefers, Daniel, Kayang, Boniface B., Kanai, Tamotsu, Sato, Takaaki, Bernardi, Rafael C., Atomi, Haruyuki, Mackie, Roderick I.
Vydáno v Appl Environ Microbiol (2020)

The Structural Dynamics of the Flavivirus Fusion Peptide–Membrane Interaction

Autor Mendes, Ygara S., Alves, Nathalia S., Souza, Theo L. F., Sousa, Ivanildo P., Bianconi, M. Lucia, Bernardi, Rafael C., Pascutti, Pedro G., Silva, Jerson L., Gomes, Andre M. O., Oliveira, Andréa C.
Vydáno 2012

Ultrastable cellulosome-adhesion complex tightens under load

Autor Schoeler, Constantin, Malinowska, Klara H., Bernardi, Rafael C., Milles, Lukas F., Jobst, Markus A., Durner, Ellis, Ott, Wolfgang, Fried, Daniel B., Bayer, Edward A., Schulten, Klaus, Gaub, Hermann E., Nash, Michael A.
Vydáno v Nat Commun (2014)

NAMD goes quantum: An integrative suite for QM/MM simulations

Autor Melo, Marcelo C. R., Bernardi, Rafael C., Rudack, Till, Scheurer, Maximilian, Riplinger, Christoph, Phillips, James C., Maia, Julio D. C., Rocha, Gerd B., Ribeiro, João V., Stone, John E., Neese, Frank, Schulten, Klaus, Luthey-Schulten, Zaida
Vydáno v Nat Methods (2018)

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Autor Phillips, James C., Hardy, David J., Maia, Julio D. C., Stone, John E., Ribeiro, João V., Bernardi, Rafael C., Buch, Ronak, Fiorin, Giacomo, Hénin, Jérôme, Jiang, Wei, McGreevy, Ryan, Melo, Marcelo C. R., Radak, Brian K., Skeel, Robert D., Singharoy, Abhishek, Wang, Yi, Roux, Benoît, Aksimentiev, Aleksei, Luthey-Schulten, Zaida, Kalé, Laxmikant V., Schulten, Klaus, Chipot, Christophe, Tajkhorshid, Emad
Vydáno v J Chem Phys (2020)