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Ultra-Fast Evaluation of Protein Energies Directly from Sequence
2006
PLoS Computational Biology
Preserved Fulltext
The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. ...
Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. ...
GG, FZ, GC, DM, and AEK analyzed the data. SRL participated in intellectual discussions. GG and AEK wrote the paper.
PLoS Funding. ...
doi:10.1371/journal.pcbi.0020063
pmid:16789811
pmcid:PMC1479088
fatcat:k6qnybbkdfbpbc6422pxk7dnim
Ultra-fast Evaluation of Protein Energies Directly from Sequence
2005
PLoS Computational Biology
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The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. ...
Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. ...
GG, FZ, GC, DM, and AEK analyzed the data. SRL participated in intellectual discussions. GG and AEK wrote the paper.
PLoS Funding. ...
doi:10.1371/journal.pcbi.0020063.eor
fatcat:shyxuf6ngbcxfluweotmjjx6la
Coarse-Graining Protein Energetics in Sequence Variables
2005
Physical Review Letters
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We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. ...
The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. ...
The technique of cluster expansion (CE) [10, 11] has proven extremely useful for rapidly evaluating the energies of alloys and searching for low-energy configurations. ...
doi:10.1103/physrevlett.95.148103
pmid:16241695
fatcat:7lqghxta5nfvzmeaa5jggl2r2u
ACE: adaptive cluster expansion for maximum entropy graphical model inference
[article]
2016
bioRxiv
pre-print
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Here we describe the adaptive cluster expansion (ACE) method to quickly and accurately infer Ising or Potts models based on correlation data. ...
We illustrate this method on a variety of biological and artificial data sets and compare it to state-of-the-art approximate methods such as Gaussian and pseudo-likelihood inference.We show that ACE accurately ...
Murakowski for his contribution to the development of the partition function expansion, and U. Ferrari and H. Jacquin for useful discussions. Funding S.C. is funded by ANR-13-BS04-0012-01 (Coevstat). ...
doi:10.1101/044677
fatcat:ksiiy2onzbbhnns2ej3nfepqfa
ACE: adaptive cluster expansion for maximum entropy graphical model inference
2016
Bioinformatics
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Here we describe the adaptive cluster expansion (ACE) method to quickly and accurately infer Ising or Potts models based on correlation data. ...
We illustrate this method on a variety of biological and artificial data sets and compare it to state-of-the-art approximate methods such as Gaussian and pseudo-likelihood inference. ...
Murakowski for his contribution to the development of the partition function expansion, and U. Ferrari and H. Jacquin for useful discussions. Funding S.C. is funded by ANR-13-BS04-0012-01 (Coevstat). ...
doi:10.1093/bioinformatics/btw328
pmid:27329863
fatcat:2gp6mmpysbftvh7iqecz5t3pee
Algorithms for protein design
2016
Current Opinion in Structural Biology
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We conclude with a list of algorithmic challenges in computational protein design that we believe will be especially important for the design of therapeutic proteins and protein assemblies. : Proof of ...
Improving both the model and the algorithm in tandem is essential to improving the success rate of current programs, and here we review recent developments in algorithms for protein design, emphasizing ...
Acknowledgements We sincerely apologize to the many authors of outstanding work that was overlooked or not included in this review because of space limitations. ...
doi:10.1016/j.sbi.2016.03.006
pmid:27086078
pmcid:PMC5065368
fatcat:fdpilhtu3zbrrbnmkc7nvytjri
Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications
[chapter]
2017
Annual Reports in Computational Chemistry
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The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. ...
In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model ...
Computation Resource (NBCR), San Diego Supercomputer Center through the Extreme Science and Engineering Discovery Environment (Awards TG-MCA93S013 and TG-MCB140011), and the National Energy Research Scientific ...
doi:10.1016/bs.arcc.2017.06.005
pmid:29720925
pmcid:PMC5927394
fatcat:2wa5f7g4qjgwbdh753i522amg4
FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations
1997
Journal of Computational Chemistry
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Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. ...
To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-Ž .w adapted multipole method SAMM C. Niedermeier and P. ...
to the diligent choice of structural units and of optimally compact clusters the SAMM method provides a further means to reduce the approximation error connected with the truncated multipole expansions ...
doi:10.1002/(sici)1096-987x(19971115)18:14<1729::aid-jcc3>3.0.co;2-m
fatcat:zeb3vszvk5fntmqn4xahsvycq4
Key interaction patterns in proteins revealed by cluster expansion of the partition function
[article]
2022
arXiv
pre-print
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To achieve this goal, we employed a cluster expansion of the partition function in the space of sequences and evaluated numerically the statistical importance of each cluster. ...
We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence design. ...
cluster expansion and to the saddle point approximation discussed above. ...
arXiv:2204.04030v1
fatcat:if4tsldjjrarxc7jh44mpvczh4
Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs
2017
Journal of Chemical Physics
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In water clusters ranging in size up to (H 2 O) 37 , four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of ...
To predict relative energies of (H 2 O) 20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the ...
Errors as a function of cluster size are plotted in Fig. 5 , for both three-and four-body expansions. All calculations are CP-corrected. ...
doi:10.1063/1.4986110
pmid:29096456
fatcat:rbcfxg5lpjfi7jj3jzfaphfvha
Understanding the many-body expansion for large systems. II. Accuracy considerations
2016
Journal of Chemical Physics
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In applications to a sequence of water clusters, (H 2 O) N =6−55 described at the B3LYP/cc-pVDZ level, we obtain mean absolute errors (MAEs) per H 2 O monomer of ∼1.0 kcal/mol for two-body expansions, ...
To complement our study of the role of finite precision in electronic structure calculations based on a truncated many-body expansion (MBE, or "n-body expansion"), we examine the accuracy of such methods ...
In short, the results are rather erratic, and in none of the six basis sets tested does charge embedding consistently reduce the errors for two-, three-, or four-body expansions. ...
doi:10.1063/1.4947087
pmid:27131529
fatcat:jaqffpzxqvgcrlssqioon4cheq
Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case
2011
Journal of Chemical Physics
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The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions. ...
We find that the sum of the pairwise interaction energies approximates the total binding energy to ∼82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. ...
ACKNOWLEDGMENTS We thank the National Institutes of Health (Grant Nos. GM044974 and GM066689) for funding the present research. Helpful communication with Professor Alan E. ...
doi:10.1063/1.3624750
pmid:21895219
pmcid:PMC3182082
fatcat:o7reji456vf5zju7j623lmdqdq
Analysis of computational models for an accurate study of electronic excitations in GFP
2015
Physical Chemistry, Chemical Physics - PCCP
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The accuracy of PERI-CC2 is successfully assessed against RVS-CC2 for GFP model clusters and subsequently applied to a whole protein model. ...
In addition, the RI approximation has also been applied. A critical discussion of the error introduced by reducing the virtual space is found in ref. 24 . ...
addressed because of a reduced computational cost, which is gained by a slight loss of error control. ...
doi:10.1039/c4cp04524f
pmid:25494098
fatcat:pugwr2toqfc3hhxyfs4czt4akq
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
2005
Bioinformatics
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Availability: A limited version of the software for the real spherical harmonics expansion of a set of points in PDB format is freely available upon request from the authors. ...
As shape plays a crucial role in biomolecular recognition and function, the examination and development of shape description and comparison techniques is likely to be of prime importance for understanding ...
Hierarchical clustering of the real spherical expansion coefficients for 16 different conformations of NAD and 25 different conformations of ATP taken from a set of low-sequence-similarity proteins with ...
doi:10.1093/bioinformatics/bti337
pmid:15728116
fatcat:istd2npdufgivppedheiwi6iim
Gaussian Accelerated Molecular Dynamics in NAMD
2016
Journal of Chemical Theory and Computation
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GaMD implemented in the scalable NAMD is widely applicable to enhanced sampling and free energy calculations of large biomolecules. ...
free energy profiles of proteins and other large biomolecules, which solves a long-standing energetic reweighting problem of the previous aMD method. ...
In order to reduce the energetic noise, the ensemble-averaged reweighting factor can be approximated using cumulant expansion: 16 ∑ β ⟨ ⟩ = ! ...
doi:10.1021/acs.jctc.6b00931
pmid:28034310
pmcid:PMC5743237
fatcat:zhp3rlzkvvf4xjwpmrkxsrzkku
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