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Title: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Abstract

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. This work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. Finally, the latest best-in-class compressed trajectory storage format is supported.

Authors:
ORCiD logo; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1252791
Alternate Identifier(s):
OSTI ID: 1376606
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
SoftwareX
Additional Journal Information:
Journal Name: SoftwareX Journal Volume: 1-2 Journal Issue: C; Journal ID: ISSN 2352-7110
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; GPU; SIMD; Free energy

Citation Formats

Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, and Lindahl, Erik. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. United States: N. p., 2015. Web. doi:10.1016/j.softx.2015.06.001.
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Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, & Lindahl, Erik. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. United States. https://doi.org/10.1016/j.softx.2015.06.001
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Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, and Lindahl, Erik. Tue . "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers". United States. https://doi.org/10.1016/j.softx.2015.06.001.
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@article{osti_1252791,
title = {GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
abstractNote = {GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. This work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. Finally, the latest best-in-class compressed trajectory storage format is supported.},
doi = {10.1016/j.softx.2015.06.001},
journal = {SoftwareX},
number = C,
volume = 1-2,
place = {United States},
year = {Tue Sep 01 00:00:00 EDT 2015},
month = {Tue Sep 01 00:00:00 EDT 2015}
}
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https://doi.org/10.1016/j.softx.2015.06.001
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Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics
journal, August 2019

  • Wang, Yihang; Ribeiro, João Marcelo Lamim; Tiwary, Pratyush
  • Nature Communications, Vol. 10, Issue 1
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Unique structure and function of viral rhodopsins
journal, October 2019

  • Bratanov, Dmitry; Kovalev, Kirill; Machtens, Jan-Philipp
  • Nature Communications, Vol. 10, Issue 1
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Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin
journal, November 2019

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels
journal, July 2018

Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system
journal, June 2019

  • Hughes, Gareth W.; Hall, Stephen C. L.; Laxton, Claire S.
  • Nature Microbiology, Vol. 4, Issue 10
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The synergic effect of water and biomolecules in intracellular phase separation
journal, July 2019

  • Ribeiro, Sara S.; Samanta, Nirnay; Ebbinghaus, Simon
  • Nature Reviews Chemistry, Vol. 3, Issue 9
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Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3A receptor
journal, October 2018

De novo design of potent and selective mimics of IL-2 and IL-15
journal, January 2019

Conformation space of a heterodimeric ABC exporter under turnover conditions
journal, July 2019

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes
journal, September 2017

Probing the transition state in enzyme catalysis by high-pressure NMR dynamics
journal, June 2019

New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
journal, February 2017

  • Ishchenko, A.; Round, E.; Borshchevskiy, V.
  • Scientific Reports, Vol. 7, Issue 1
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Design of electric field controlled molecular gates mounted on metal–organic frameworks
journal, January 2017

  • Tam, Benjamin; Yazaydin, Ozgur
  • Journal of Materials Chemistry A, Vol. 5, Issue 18
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Atomistic characterization of collective protein–water–membrane dynamics
journal, January 2019

  • Päslack, Christopher; Schäfer, Lars V.; Heyden, Matthias
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 29
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Influence of polar co-solutes and salt on the hydration of lipid membranes
journal, January 2019

  • Wolde-Kidan, Amanuel; Pham, Quoc Dat; Schlaich, Alexander
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 31
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Sulfur-substitution-induced base flipping in the DNA duplex
journal, January 2019

  • Sun, Zhaoxi; Wang, Xiaohui; Zhang, John Z. H.
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 27
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Two dimensional diffusion-controlled triplet–triplet annihilation kinetics
journal, January 2019

  • Gschwend, Grégoire C.; Kazmierczak, Morgan; Olaya, Astrid J.
  • Chemical Science, Vol. 10, Issue 32
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Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method
journal, January 2019

  • Zhang, Wenjing; Wu, Haimei; Zhang, Rongkai
  • Chemical Science, Vol. 10, Issue 33
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Relationship between pore size and reversible and irreversible immobilization of ionic liquid electrolytes in porous carbon under applied electric potential
journal, October 2016

  • Mahurin, Shannon M.; Mamontov, Eugene; Thompson, Matthew W.
  • Applied Physics Letters, Vol. 109, Issue 14
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Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine
journal, October 2016

  • Nys, Mieke; Wijckmans, Eveline; Farinha, Ana
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 43
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Combined molecular dynamics and neural network method for predicting protein antifreeze activity
journal, December 2018

  • Kozuch, Daniel J.; Stillinger, Frank H.; Debenedetti, Pablo G.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 52
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The role of gelsolin domain 3 in familial amyloidosis (Finnish type)
journal, June 2019

  • Zorgati, Habiba; Larsson, Mårten; Ren, Weitong
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 28
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Identification of evolutionary and kinetic drivers of NAD-dependent signaling
journal, July 2019

  • Bockwoldt, Mathias; Houry, Dorothée; Niere, Marc
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 32
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Inward-facing conformation of a multidrug resistance MATE family transporter
journal, June 2019

  • Zakrzewska, Sandra; Mehdipour, Ahmad Reza; Malviya, Viveka Nand
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 25
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Ion-Induced Soot Nucleation Using a New Potential for Curved Aromatics
journal, January 2019

  • Bowal, Kimberly; Martin, Jacob W.; Misquitta, Alston J.
  • Combustion Science and Technology, Vol. 191, Issue 5-6
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Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)
journal, April 2020

Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis
journal, January 2017

  • Pandey, Bharati; Grover, Sonam; Tyagi, Chetna
  • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 2
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Triazavirine supramolecular complexes as modifiers of the peptide oligomeric structure
journal, August 2017

  • Shvetsov, Alexey V.; Zabrodskaya, Yana A.; Nekrasov, Peter A.
  • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 10
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Simulation of protein diffusion: a sensitive probe of protein–solvent interactions
journal, April 2018

Novel coumarin derivatives as potent acetylcholinesterase inhibitors: insight into efficacy, mode and site of inhibition
journal, May 2018

  • Baruah, Prayasee; Basumatary, Grace; Yesylevskyy, Semen O.
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 7
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Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study
journal, November 2018

  • Ramya Chandar Charles, M.; Hsieh, Hsing-Pang; Selvaraj Coumar, Mohane
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 10
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In silico site-directed mutagenesis of neutralizing mAb 4C4 and analysis of its interaction with G-H loop of VP1 to explore its therapeutic applications against FMD
journal, November 2018

  • Sahu, Tanmaya Kumar; Pradhan, Dibyabhaba; Rao, Atmakuri Ramakrishna
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 10
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Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ 42 aggregation and protofibril destabilization: A molecular dynamics simulation study
journal, December 2018

  • Saini, Rajneet Kaur; Shuaib, Suniba; Goyal, Deepti
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 12
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3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes
journal, December 2018

  • Lopes-Rodrigues, Maximilien; Zanuy, David; Alemán, Carlos
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 15
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Deciphering foot-and-mouth disease (FMD) virus–host tropism
journal, February 2019

Characterization of heterogeneous intermediate ensembles on the guanidinium chloride-induced unfolding pathway of β-lactoglobulin
journal, March 2019

Disease-associated mutations alter the dynamic motion of the N-terminal domain of the human cardiac ryanodine receptor
journal, March 2019

Inhibition of Alzheimer’s amyloid-β 42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations
journal, May 2019

Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway
journal, May 2019

Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi : an example of cooperative behavior
journal, June 2019

A mechanistic approach to understand the allosteric reverse signaling by selective and trapping poly(ADP-ribose) polymerase 1 (PARP-1) inhibitors
journal, June 2019

Identification of cisplatin-binding sites on the large cytoplasmic loop of the Na + /K + -ATPase
journal, January 2018

  • Šeflová, Jaroslava; Čechová, Petra; Štenclová, Tereza
  • Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 33, Issue 1
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Molecular modeling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime, 4-PA, 2-PAM, and obidoxime with VX-inhibited human acetylcholinesterase: a near attack conformation approach
journal, January 2019

  • da Silva, Jorge Alberto Valle; Nepovimova, Eugenie; Ramalho, Teodorico Castro
  • Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 34, Issue 1
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Sodium-salt adduct fullerenes prevent self-association and amyloid β fibril formation: molecular dynamics approach
journal, April 2020

Adevonin, a novel synthetic antimicrobial peptide designed from the Adenanthera pavonina trypsin inhibitor (ApTI) sequence
journal, November 2018

  • Rodrigues, Mayara S.; Oliveira, Caio F. R. de; Almeida, Luís H. O.
  • Pathogens and Global Health, Vol. 112, Issue 8
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Conduction through a narrow inward-rectifier K + channel pore
journal, September 2019

  • Bernsteiner, Harald; Zangerl-Plessl, Eva-Maria; Chen, Xingyu
  • The Journal of General Physiology, Vol. 151, Issue 10
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TADOSS: computational estimation of tandem domain swap stability
journal, November 2018

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters
journal, April 2018

Aspirin locally disrupts the liquid-ordered phase
journal, February 2018

  • Alsop, Richard J.; Himbert, Sebastian; Dhaliwal, Alexander
  • Royal Society Open Science, Vol. 5, Issue 2
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Asymmetric nucleophilic fluorination under hydrogen bonding phase-transfer catalysis
journal, May 2018

Nano-metering of Solvated Biomolecules Or Nanoparticles from Water Self-Diffusivity in Bio-inspired Nanopores
journal, October 2019

  • Bergamasco, Luca; Alberghini, Matteo; Fasano, Matteo
  • Nanoscale Research Letters, Vol. 14, Issue 1
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Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
journal, December 2016

  • Lima, Rayane Nunes; Faheem, Muhammad; Barbosa, João Alexandre Ribeiro Gonçalves
  • BMC Bioinformatics, Vol. 17, Issue S18
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Generation of dual specific bivalent BiTEs (dbBIspecific T-cell engaging antibodies) for cellular immunotherapy
journal, September 2019

Porcine parvovirus VP1/VP2 on a time series epitope mapping: exploring the effects of high hydrostatic pressure on the immune recognition of antigens
journal, June 2019

Molmil: a molecular viewer for the PDB and beyond
journal, August 2016

  • Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R.
  • Journal of Cheminformatics, Vol. 8, Issue 1
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Systematic exploration of multiple drug binding sites
journal, December 2017

  • Bálint, Mónika; Jeszenői, Norbert; Horváth, István
  • Journal of Cheminformatics, Vol. 9, Issue 1
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Engineering E. coli cell surface in order to develop a one-step purification method for recombinant proteins
journal, June 2018

Excessive aggregation of membrane proteins in the Martini model
journal, November 2017

A structural model of the human serotonin transporter in an outward-occluded state
journal, June 2019

Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence
journal, September 2016

Multiple C2 domains and transmembrane region proteins ( MCTP s) tether membranes at plasmodesmata
journal, July 2019

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System
journal, August 2019

  • Pedersen, Dennis V.; Gadeberg, Trine A. F.; Thomas, Caroline
  • Frontiers in Immunology, Vol. 10
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Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale
journal, November 2019

  • Fernández-Quintero, Monica L.; Math, Barbara A.; Loeffler, Johannes R.
  • Frontiers in Immunology, Vol. 10
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Unusual Placement of an EBV Epitope into the Groove of the Ankylosing Spondylitis-Associated HLA-B27 Allele Allows CD8+ T Cell Activation
journal, June 2019

  • Tedeschi, Valentina; Alba, Josephine; Paladini, Fabiana
  • Cells, Vol. 8, Issue 6
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Interaction of Mycotoxin Alternariol with Serum Albumin
journal, May 2019

  • Fliszár-Nyúl, Eszter; Lemli, Beáta; Kunsági-Máté, Sándor
  • International Journal of Molecular Sciences, Vol. 20, Issue 9
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Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide
journal, May 2019

  • Yang, Bing; Lin, Shu-Jian; Ren, Jia-Yi
  • International Journal of Molecular Sciences, Vol. 20, Issue 10
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Conformational Insight on WT- and Mutated-EGFR Receptor Activation and Inhibition by Epigallocatechin-3-Gallate: Over a Rational Basis for the Design of Selective Non-Small-Cell Lung Anticancer Agents
journal, March 2020

  • Minnelli, Cristina; Laudadio, Emiliano; Mobbili, Giovanna
  • International Journal of Molecular Sciences, Vol. 21, Issue 5
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Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3
text, January 2018

Cryo-EM structure of the mechanically activated ion channel OSCA1.2
journal, November 2018

  • Jojoa-Cruz, Sebastian; Saotome, Kei; Murthy, Swetha E.
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The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
journal, January 2019

  • Lloyd Evans, Dyfed; Hlongwane, Thandekile Thandiwe; Joshi, Shailesh V.
  • PeerJ, Vol. 7
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Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture
journal, May 2019

  • Bandara, Asanga; Panahi, Afra; Pantelopulos, George A.
  • The Journal of Chemical Physics, Vol. 150, Issue 20
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Microwave heating and non-thermal effects of sodium chloride aqueous solution
journal, September 2019

Targeting the protein-protein interface pocket of Aurora-A-TPX2 complex: rational drug design and validation
journal, June 2020

Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
journal, June 2020

Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2
journal, June 2020

Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb 2+ ion: a joint molecular dynamics simulation and experimental study
journal, April 2020

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors
journal, May 2020

Molecular mechanism of light-driven sodium pumping
journal, May 2020

Molecular dynamics simulations of CO 2 permeation through ionic liquids confined in γ-alumina nanopores
journal, July 2018

In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of Acinetobacter baumannii
journal, April 2017

  • Verma, Privita; Tiwari, Monalisa; Tiwari, Vishvanath
  • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 5
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New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer’s disease: Synthesis, molecular modeling, NMR, and biological evaluation
journal, November 2017

  • Ferreira Neto, Denise Cristian; Alencar Lima, Josélia; Sobreiro Francisco Diz de Almeida, Joyce
  • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 15
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Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: a therapeutic target for prostate cancer
journal, February 2018

  • Kumar, Rakesh; Maurya, Ranjana; Saran, Shweta
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 3
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A coarse-grained model for PCL: conformation, self-assembly of MePEG-b-PCL amphiphilic diblock copolymers
journal, September 2016

Insights into the binding of agonist and antagonist to TAS2R16 receptor: a molecular simulation study
journal, September 2017

Identifying novel small molecule antagonists for mLST8 protein using computational approaches
journal, October 2017

  • Sapam, Tuleshwori Devi; Velmurugan Ilavarasi, Anbumani; Palaka, Bhagath Kumar
  • Journal of Receptors and Signal Transduction, Vol. 38, Issue 1
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Investigating Ebola virus pathogenicity using molecular dynamics
journal, August 2017

Understanding the stability of polypeptide membranes in ionic liquids: a theoretical molecular dynamics study
journal, January 2019

  • Alves, Eyber Domingos; Oliveira, Leonardo Bruno Assis; Colherinhas, Guilherme
  • New Journal of Chemistry, Vol. 43, Issue 25
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A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates
journal, June 2019

  • Rao, Shanlin; Klesse, Gianni; Stansfeld, Phillip J.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 28
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Validation of NAD synthase inhibitors for inhibiting the cell viability of Leishmania donovani : In silico and in vitro approach
journal, January 2019

  • Mandal, Haraprasad; Vijayakumar, Saravanan; Yadav, Shalini
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 17
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Machine Learning From Molecular Dynamics Trajectories to Predict Caspase-8 Inhibitors Against Alzheimer’s Disease
journal, July 2019

Topological Water Network Analysis Around Amino Acids
journal, July 2019

Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3
text, January 2018

Ion-Induced Soot Nucleation Using a New Potential for Curved Aromatics
text, January 2019

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations
journal, December 2019

Optimizing Antimicrobial Peptide Dendrimers in Chemical Space
journal, June 2018

  • Siriwardena, Thissa N.; Capecchi, Alice; Gan, Bee-Ha
  • Angewandte Chemie International Edition, Vol. 57, Issue 28
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A Stereochemically Driven Supramolecular Polymerisation
journal, May 2018

  • Tasca, Elisamaria; D'Abramo, Marco; Galantini, Luciano
  • Chemistry - A European Journal, Vol. 24, Issue 32
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Novel analogs of sulfasalazine as system x c − antiporter inhibitors: Insights from the molecular modeling studies
journal, June 2019

  • Patel, Dhavalkumar; Kharkar, Prashant S.; Gandhi, Neha S.
  • Drug Development Research, Vol. 80, Issue 6
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Antimicrobial Peptide Dendrimer Chimera
journal, April 2019

  • Siriwardena, Thissa N.; Lüscher, Alexandre; Köhler, Thilo
  • Helvetica Chimica Acta, Vol. 102, Issue 4
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Disease‐associated missense variants in ZBTB18 disrupt DNA binding and impair the development of neurons within the embryonic cerebral cortex
journal, July 2019

  • Hemming, Isabel A.; Clément, Olivier; Gladwyn‐Ng, Ivan E.
  • Human Mutation, Vol. 40, Issue 10
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CHARMM-GUI 10 years for biomolecular modeling and simulation: Biomolecular Modeling and Simulation
journal, November 2016

  • Jo, Sunhwan; Cheng, Xi; Lee, Jumin
  • Journal of Computational Chemistry, Vol. 38, Issue 15
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Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether
journal, August 2019

  • Takeda, Kosuke; Fujimoto, Kazushi; Yoshii, Noriyuki
  • Journal of Computational Chemistry, Vol. 40, Issue 31
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Dual inhibition of EGFR and MET by Echinatin retards cell growth and induces apoptosis of lung cancer cells sensitive or resistant to gefitinib
journal, November 2019

  • Oh, Ha‐Na; Lee, Mee‐Hyun; Kim, Eunae
  • Phytotherapy Research, Vol. 34, Issue 2
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Mixed Fluorinated/Hydrogenated Self‐Assembled Monolayer‐Protected Gold Nanoparticles: In Silico and In Vitro Behavior
journal, April 2019

Exploring the Viral Channel KcvPBCV-1 Function via Computation
journal, February 2018

  • Andersson, Alma E. V.; Kasimova, Marina A.; Delemotte, Lucie
  • The Journal of Membrane Biology, Vol. 251, Issue 3
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HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data
journal, August 2018

  • Carrillo-Tripp, Mauricio; Alvarez-Rivera, Leonardo; Lara-Ramírez, Omar Israel
  • Journal of Computer-Aided Molecular Design, Vol. 32, Issue 8
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FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations
journal, April 2019

Molecular dynamics based antimicrobial activity descriptors for synthetic cationic peptides
journal, February 2019

  • Biswal, Malay Ranjan; Rai, Sandhya; Prakash, Meher K.
  • Journal of Chemical Sciences, Vol. 131, Issue 2
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Study on a Biomimetic Enzyme-Linked Immunosorbent Assay for Rapid Detection of Flumequine in Animal Foods
journal, November 2019

Multiscale molecular dynamics simulations of rotary motor proteins
journal, December 2017

A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations
journal, January 2020

Structural basis for selectivity and diversity in angiotensin II receptors
journal, April 2017

  • Zhang, Haitao; Han, Gye Won; Batyuk, Alexander
  • Nature, Vol. 544, Issue 7650
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Structural basis for functional interactions in dimers of SLC26 transporters
journal, May 2019

Substrate-induced conformational dynamics of the dopamine transporter
journal, June 2019

A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases
journal, July 2019

Site-specific ubiquitylation and SUMOylation using genetic-code expansion and sortase
journal, February 2019

  • Fottner, Maximilian; Brunner, Andreas-David; Bittl, Verena
  • Nature Chemical Biology, Vol. 15, Issue 3
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Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
journal, February 2018

Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis
journal, March 2018

Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist
journal, June 2018

  • Spahn, Viola; Del Vecchio, Giovanna; Rodriguez-Gaztelumendi, Antonio
  • Scientific Reports, Vol. 8, Issue 1
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Membrane-Modulating Drugs can Affect the Size of Amyloid-β25–35 Aggregates in Anionic Membranes
journal, August 2018

Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods
journal, November 2018

Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain
journal, February 2019

Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics
journal, December 2018

  • Sheik Amamuddy, Olivier; Bishop, Nigel T.; Tastan Bishop, Özlem
  • Scientific Reports, Vol. 8, Issue 1
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Theoretical analysis on thermodynamic stability of chignolin
journal, March 2019

Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis
journal, July 2019

  • Barruetabeña, Nerea; Alonso-Lerma, Borja; Galera-Prat, Albert
  • Communications Chemistry, Vol. 2, Issue 1
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Insights from molecular dynamics simulations for computational protein design
journal, January 2017

  • Childers, Matthew Carter; Daggett, Valerie
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Coupling between the mesoscopic dynamics and shear stress of a room-temperature ionic liquid
journal, January 2018

  • Yamaguchi, Tsuyoshi
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Solvation of Al 3+ cations in bulk and confined protic ionic liquids: a computational study
journal, January 2018

  • Gómez-González, Víctor; Docampo-Álvarez, Borja; Montes-Campos, Hadrián
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Computational microscopy study of the granular structure and pH dependence of PEDOT:PSS
journal, January 2019

  • Modarresi, Mohsen; Franco-Gonzalez, Juan Felipe; Zozoulenko, Igor
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 12
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Cross-linker effect on solute adsorption in swollen thermoresponsive polymer networks
journal, January 2019

  • Milster, Sebastian; Chudoba, Richard; Kanduč, Matej
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 12
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Elucidating the role of surface chemistry on cationic phosphorus dendrimer–siRNA complexation
journal, January 2018

  • Deriu, Marco A.; Tsapis, Nicolas; Noiray, Magali
  • Nanoscale, Vol. 10, Issue 23
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Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase
journal, January 2018

  • Barrozo, Alexandre; Liao, Qinghua; Esguerra, Mauricio
  • Organic & Biomolecular Chemistry, Vol. 16, Issue 12
  • DOI: 10.1039/c8ob00312b

Atomistic investigation of an Iowa Amyloid-β trimer in aqueous solution
journal, January 2018

  • Ngo, Son Tung; Thu Phung, Huong Thi; Vu, Khanh B.
  • RSC Advances, Vol. 8, Issue 73
  • DOI: 10.1039/c8ra07615d

Growth of wormlike micelles of surfactant induced by embedded polymer: role of polymer chain length
journal, January 2018

  • Kwiatkowski, Alexander L.; Molchanov, Vyacheslav S.; Sharma, Hari
  • Soft Matter, Vol. 14, Issue 23
  • DOI: 10.1039/c8sm00776d

Elucidating the key role of fluorine in improving the charge mobility of electron acceptors for non-fullerene organic solar cells by multiscale simulations
journal, January 2018

  • Yao, Chuang; Peng, Cheng; Yang, Yezi
  • Journal of Materials Chemistry C, Vol. 6, Issue 18
  • DOI: 10.1039/c8tc01315b

Redesign and engineering of a dioxygenase targeting biocatalytic synthesis of 5-hydroxyl leucine
journal, January 2019

  • Sun, Dengyue; Gao, Dengke; Liu, Xin
  • Catalysis Science & Technology, Vol. 9, Issue 8
  • DOI: 10.1039/c9cy00110g

Affinity of fentanyl and its derivatives for the σ 1 -receptor
journal, January 2019

  • Lipiński, Piotr F. J.; Szűcs, Edina; Jarończyk, Małgorzata
  • MedChemComm, Vol. 10, Issue 7
  • DOI: 10.1039/c9md00222g

Detecting early stage structural changes in wild type, pathogenic and non-pathogenic prion variants using Markov state model
journal, January 2019

  • Jani, Vinod; Sonavane, Uddhavesh; Joshi, Rajendra
  • RSC Advances, Vol. 9, Issue 25
  • DOI: 10.1039/c9ra01507h

Large scale relative protein ligand binding affinities using non-equilibrium alchemy
journal, January 2020

  • Gapsys, Vytautas; Pérez-Benito, Laura; Aldeghi, Matteo
  • Chemical Science, Vol. 11, Issue 4
  • DOI: 10.1039/c9sc03754c

A comparative computational study of coarse-grained and all-atom water models in shock Hugoniot states
journal, April 2018

  • Min, Sa Hoon; Berkowitz, Max L.
  • The Journal of Chemical Physics, Vol. 148, Issue 14
  • DOI: 10.1063/1.5011968

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study
journal, June 2018

  • Grillo, Damián A.; Albano, Juan M. R.; Mocskos, Esteban E.
  • The Journal of Chemical Physics, Vol. 148, Issue 21
  • DOI: 10.1063/1.5028377

Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides
journal, October 2017

  • Senju, Yosuke; Kalimeri, Maria; Koskela, Essi V.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 43
  • DOI: 10.1073/pnas.1705032114

Computational discovery of chemically patterned surfaces that effect unique hydration water dynamics
journal, July 2018

  • Monroe, Jacob I.; Shell, M. Scott
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 32
  • DOI: 10.1073/pnas.1807208115

The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist
journal, March 2020

  • Mafi, Amirhossein; Kim, Soo-Kyung; Goddard, William A.
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 11
  • DOI: 10.1073/pnas.1910006117

Determination and evaluation of the nonadditivity in wetting of molecularly heterogeneous surfaces
journal, December 2019

  • Luo, Zhi; Murello, Anna; Wilkins, David M.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 51
  • DOI: 10.1073/pnas.1916180116

N-terminal Prion Protein Peptides (PrP(120–144)) Form Parallel In-register β-Sheets via Multiple Nucleation-dependent Pathways
journal, August 2016

  • Wang, Yiming; Shao, Qing; Hall, Carol K.
  • Journal of Biological Chemistry, Vol. 291, Issue 42
  • DOI: 10.1074/jbc.m116.744573

Structural and thermodynamic insights into β-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua
journal, April 2018

  • Abe, Koichi; Sunagawa, Naoki; Terada, Tohru
  • Journal of Biological Chemistry, Vol. 293, Issue 23
  • DOI: 10.1074/jbc.ra117.001536

Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding
journal, October 2018

  • Ge, Yunhui; Borne, Elias; Stewart, Shannon
  • Journal of Biological Chemistry, Vol. 293, Issue 51
  • DOI: 10.1074/jbc.ra118.004909

Identification, characterization, and structural analyses of a fungal endo-β-1,2-glucanase reveal a new glycoside hydrolase family
journal, March 2019

  • Tanaka, Nobukiyo; Nakajima, Masahiro; Narukawa-Nara, Megumi
  • Journal of Biological Chemistry, Vol. 294, Issue 19
  • DOI: 10.1074/jbc.ra118.007087

A two-component protease in Methylorubrum extorquens with high activity toward the peptide precursor of the redox cofactor pyrroloquinoline quinone
journal, August 2019

  • Martins, Ana M.; Latham, John A.; Martel, Paulo J.
  • Journal of Biological Chemistry, Vol. 294, Issue 41
  • DOI: 10.1074/jbc.ra119.009684

Impact of key residues within chloroplast thioredoxin- f on recognition for reduction and oxidation of target proteins
journal, October 2019

  • Yokochi, Yuichi; Sugiura, Kazunori; Takemura, Kazuhiro
  • Journal of Biological Chemistry, Vol. 294, Issue 46
  • DOI: 10.1074/jbc.ra119.010401

Molecular dynamics perspective on the thermal stability of mandelate racemase
journal, January 2018

Pharmacophore-based virtual screening approach for identification of potent natural modulatory compounds of human Toll-like receptor 7
journal, January 2019

  • Gupta, Chhedi Lal; Babu Khan, Mohd.; Ampasala, Dinakara Rao
  • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 18
  • DOI: 10.1080/07391102.2018.1559098

Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist
journal, February 2020

Conformational tuning of a DNA-bound transcription factor
journal, April 2019

  • Sicoli, Giuseppe; Vezin, Hervé; Ledolter, Karin
  • Nucleic Acids Research, Vol. 47, Issue 10
  • DOI: 10.1093/nar/gkz291

Mechanically inferior constituents in spider silk result in mechanically superior fibres by adaptation to harsh hydration conditions: a molecular dynamics study
journal, July 2018

  • Kim, Yoonjung; Lee, Myeongsang; Baek, Inchul
  • Journal of The Royal Society Interface, Vol. 15, Issue 144
  • DOI: 10.1098/rsif.2018.0305

An unexpected dynamic binding mode between coagulation factor X and Rivaroxaban reveals importance of flexibility in drug binding
journal, June 2019

  • Qu, Si‐Ying; Xu, Qin; Wu, Wenman
  • Chemical Biology & Drug Design, Vol. 94, Issue 3
  • DOI: 10.1111/cbdd.13568

Structure of monomeric full-length ARC sheds light on molecular flexibility, protein interactions, and functional modalities
journal, September 2018

  • Hallin, Erik I.; Eriksen, Maria S.; Baryshnikov, Sergei
  • Journal of Neurochemistry, Vol. 147, Issue 3
  • DOI: 10.1111/jnc.14556

Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation
journal, August 2019

Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation
journal, January 2020

  • Behring, Jessica B.; van der Post, Sjoerd; Mooradian, Arshag D.
  • Science Signaling, Vol. 13, Issue 615
  • DOI: 10.1126/scisignal.aay7315

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers
journal, November 2018

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties
journal, January 2019

  • Fernández-Quintero, Monica L.; Loeffler, Johannes R.; Kraml, Johannes
  • Frontiers in Immunology, Vol. 9
  • DOI: 10.3389/fimmu.2018.03065

The Energetic Viability of Δ1-Piperideine Dimerization in Lysine-derived Alkaloid Biosynthesis
journal, August 2018

  • Sato, Hajime; Uchiyama, Masanobu; Saito, Kazuki
  • Metabolites, Vol. 8, Issue 3
  • DOI: 10.3390/metabo8030048

Novel Hit Compounds as Putative Antifungals: The Case of Aspergillus fumigatus
journal, October 2019

  • Kritsi, Eftichia; Matsoukas, Minos-Timotheos; Potamitis, Constantinos
  • Molecules, Vol. 24, Issue 21
  • DOI: 10.3390/molecules24213853

Characterization of HIV-2 Protease Structure by Studying Its Asymmetry at the Different Levels of Protein Description
journal, November 2018

  • Ollitrault, Guillaume; Fartek, Sandrine; Descamps, Diane
  • Symmetry, Vol. 10, Issue 11
  • DOI: 10.3390/sym10110644

Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF
journal, March 2019

Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation
text, January 2020

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding
journal, November 2018

Deamidation disrupts native and transient contacts to weaken the interaction between UBC13 and RING-finger E3 ligases
journal, October 2019

  • Mohanty, Priyesh; Agrata, Rashmi; Habibullah, Batul Ismail
  • eLife, Vol. 8
  • DOI: 10.7554/elife.49223

Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations
journal, January 2019

  • Shimato, Takuya; Kasahara, Kota; Higo, Junichi
  • PeerJ Physical Chemistry, Vol. 1
  • DOI: 10.7717/peerj-pchem.4

NMR structure of the C-terminal domain of TonB protein from Pseudomonas aeruginosa
journal, January 2018

  • Oeemig, Jesper S.; Ollila, O. H. Samuli; Iwaï, Hideo
  • PeerJ, Vol. 6
  • DOI: 10.7717/peerj.5412
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