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Ultra-Fast Evaluation of Protein Energies Directly from Sequence

Gevorg Grigoryan, Fei Zhou, Steve R. Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating
2006 PLoS Computational Biology  
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

Gevorg Grigoryan, Fei Zhou, Steve R Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating
2005 PLoS Computational Biology  
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

Fei Zhou, Gevorg Grigoryan, Steve R. Lustig, Amy E. Keating, Gerbrand Ceder, Dane Morgan
2005 Physical Review Letters  
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]

John P Barton, Eleonora De Leonardis, Alice Coucke, Simona Cocco
2016 bioRxiv   pre-print
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

J. P. Barton, E. De Leonardis, A. Coucke, S. Cocco
2016 Bioinformatics  
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

Pablo Gainza, Hunter M Nisonoff, Bruce R Donald
2016 Current Opinion in Structural Biology  
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]

Yinglong Miao, J. Andrew McCammon
2017 Annual Reports in Computational Chemistry  
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

M. Eichinger, H. Grubm�ller, H. Heller, P. Tavan
1997 Journal of Computational Chemistry  
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]

M. Tajana, A. Trovato, G. Tiana
2022 arXiv   pre-print
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

Kuan-Yu Liu, John M. Herbert
2017 Journal of Chemical Physics  
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

Ka Un Lao, Kuan-Yu Liu, Ryan M. Richard, John M. Herbert
2016 Journal of Chemical Physics  
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

Melek N. Ucisik, Danial S. Dashti, John C. Faver, Kenneth M. Merz
2011 Journal of Chemical Physics  
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

Tobias Schwabe, Maarten T. P. Beerepoot, Jógvan Magnus Haugaard Olsen, Jacob Kongsted
2015 Physical Chemistry, Chemical Physics - PCCP  
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

R. J. Morris, R. J. Najmanovich, A. Kahraman, J. M. Thornton
2005 Bioinformatics  
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

Yui Tik Pang, Yinglong Miao, Yi Wang, J. Andrew McCammon
2016 Journal of Chemical Theory and Computation  
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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