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Biophysical simulations

DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation

Ghadi S. Al Hajj, Johan Pensar, Geir K. Sandve

Deciphering the relational dynamics of AF-2 domain of PAN PPAR through drug repurposing and comparative simulations

Fouzia Gul, Nousheen Parvaiz, Syed Sikander Azam

Understanding the self-assembly dynamics of A/T absent ‘four-way DNA junctions with sticky ends’ at altered physiological conditions through molecular dynamics simulations

Akanksha Singh, Ramesh Kumar Yadav, [ ... ], Umesh Yadava

Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands

Guillermo Goode-Romero, Laura Dominguez

Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands

Husnul Fuad Zein, Ibrar Alam, Piyapong Asanithi, Thana Sutthibutpong

The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics

Shivani Yaduvanshi, Rya Ero, Veerendra Kumar

Stochastic simulation algorithms for Interacting Particle Systems

Timothy C. Stutz, Alfonso Landeros, [ ... ], Kenneth Lange

Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis

Gabriel Rodrigues Coutinho Pereira, Bárbara de Azevedo Abrahim Vieira, Joelma Freire De Mesquita

Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades

Michael A. Rowland, Kevin R. Pilkiewicz, Michael L. Mayo

Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations

Arthur Voronin, Marie Weiel, Alexander Schug

BD5: An open HDF5-based data format to represent quantitative biological dynamics data

Koji Kyoda, Kenneth H. L. Ho, [ ... ], Shuichi Onami

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

Philip Horx, Armin Geyer

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

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