Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

Seeber, Michele; Felline, Angelo; Raimondi, Francesco; Muff, Stefanie; Friedman, Ran; Rao, Francesco; Caflisch, Amedeo; Fanelli, Francesca

doi:10.1002/jcc.21688

Cited by 239 publications

(267 citation statements)

References 60 publications

(120 reference statements)

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“…This can be done during post processing on the trajectory file, much like a conventional analysis tool, or on-the-fly during the simulation. Other software is available for analyzing existing trajectories [7,20,21,22,23,24] or for biasing MD simulations [15,9,25,26,27,7,6]. PLUMED 2, however, is the only code we know of that allows users to do both sets of tasks with a single syntax.…”

Section: Plumed 2 Overviewmentioning

confidence: 99%

PLUMED 2: New feathers for an old bird

Tribello

Bonomi

Branduardi

et al. 2014

Computer Physics Communications

2,634

2,841

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Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardwares, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here -a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

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Section: Plumed 2 Overviewmentioning

confidence: 99%

PLUMED 2: New feathers for an old bird

Tribello

Bonomi

Branduardi

et al. 2014

Computer Physics Communications

2,634

2,841

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“…40,41 There are several software packages available for TICA and MSM analysis. [42][43][44][45] Our calculations are done using the pyEMMA software. 42 …”

Section: Tica and Msm Analysismentioning

confidence: 99%

Markov modeling of peptide folding in the presence of protein crowders

Nilsson

Mohanty

Irbäck

2018

The Journal of Chemical Physics

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We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major freeenergy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders have a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate k u , while the folding rate k f is left largely unchanged.

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“…Pairs of snapshots were compared using the positional root mean square deviation (RMSD) upon optimal structural overlap, and clustering was performed by the Leader algorithm as implemented in the trajectory analysis program Wordom. 40 The conformations of contiguous repeat pairs were clustered as follows: the N-terminal cap and the first internal repeat (N-cap/R1); the last internal repeat and the C-terminal cap (R4/C-cap); and all the internal repeats (Rn/Rnþ1). As the pairs R1/R2, R2/R3, and R3/R4 are topologically identical, the conformations of the internal repeat pairs (R1/R2, R2/R3, and R3/R4) were collected together to increase the statistics and generate a single model for the internal repeat pair.…”

Section: Clustering Of Trajectoriesmentioning

confidence: 99%

“…40 Global entropies, calculated on all Ca atoms, were normalized by the number of residues in order to compare models of different lengths (e.g., YM 4 A and YM 4 A have 243 residues, whereas their variants Y II-M 4 A II and Y II M 4 A II have 242 residues). Local entropies were calculated for a subset of atoms spanning individual repeat dimers (i.e., N-cap/R1, R1/R2, R2/ R3, R3/R4, and R4/C-cap).…”

Section: Trajectory Analysismentioning

confidence: 99%

Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy

et al. 2012

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A multidisciplinary approach based on molecular dynamics (MD) simulations using homology models, NMR spectroscopy, and a variety of biophysical techniques was used to efficiently improve the thermodynamic stability of armadillo repeat proteins (ArmRPs). ArmRPs can form the basis of modular peptide recognition and the ArmRP version on which synthetic libraries are based must be as stable as possible. The 42-residue internal Arm repeats had been designed previously using a sequence-consensus method. Heteronuclear NMR revealed unfavorable interactions present at neutral but absent at high pH. Two lysines per repeat were involved in repulsive interactions, and stability was increased by mutating both to glutamine. Five point mutations in the capping repeats were suggested by the analysis of positional fluctuations and configurational entropy along multiple MD simulations. The most stabilizing single C-cap mutation Q240L was inferred from explicit solvent MD simulations, in which water penetrated the ArmRP. All mutants were characterized by temperature-and denaturant-unfolding studies and the improved mutants were established as monomeric species with cooperative folding and increased stability against heat and denaturant. Importantly, the mutations tested resulted in a cumulative decrease of flexibility of the folded state in silico and a cumulative increase of thermodynamic stability in vitro. The final construct has a melting temperature of about 85°C, 14.5°higher than the starting sequence. This work indicates that in silico studies in combination with heteronuclear NMR and other biophysical tools may provide a basis for successfully selecting mutations that rapidly improve biophysical properties of the target proteins.

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Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

Cited by 239 publications

References 60 publications

PLUMED 2: New feathers for an old bird

PLUMED 2: New feathers for an old bird

Markov modeling of peptide folding in the presence of protein crowders

Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy

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