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Algorithms for protein design

Pablo Gainza, Hunter M Nisonoff, Bruce R Donald
2016 Current Opinion in Structural Biology  
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  ...  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  ...  We thank Marcel Frankel, Anna Lowegard, and Jonathan Jou for comments on the manuscript, as well as Mark A Hallen for helpful discussions.  ... 
doi:10.1016/j.sbi.2016.03.006 pmid:27086078 pmcid:PMC5065368 fatcat:fdpilhtu3zbrrbnmkc7nvytjri

Conformational diversity and computational enzyme design

Jonathan K Lassila
2010 Current Opinion in Chemical Biology  
Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability.  ...  including recent advances in multistate design, backbone flexibility, and computational library design.  ...  In a different approach, a cluster-expansion method [55] was used for simultaneous design with many states to introduce backbone conformational diversity [56] and to perform negative design for specificity  ... 
doi:10.1016/j.cbpa.2010.08.010 pmid:20829099 pmcid:PMC2953567 fatcat:sphqhcyafngvvnmkehggsdgray

Prediction of secondary structure and dihedral angles in proteins

T. Zhou, N. Shu, S. Hovmoller
2008 Acta Crystallographica Section A Foundations of Crystallography  
A method for simultaneous prediction of secondary structure and dihedral angles of the polypeptide backbone in proteins is presented here.  ...  Thus, we show here for the first time that the conformations of all amino acids in proteins can be as accurately predicted as the secondary structure.  ...  refinement of structural models as well as for quantitative phase analysis.  ... 
doi:10.1107/s0108767308092751 fatcat:7delip4p5bcgpfxrnlpsnu2cyy

Prediction and simulation of motion in pairs of transmembrane -helices

A. Enosh, S. J. Fleishman, N. Ben-Tal, D. Halperin
2007 Bioinformatics  
We have developed an algorithm for predicting and simulating motion in TM proteins of the a-helix bundle type.  ...  Thus, developing an automated method for predicting and simulating motion in this class of proteins should result in an increased level of understanding of crucial physiological mechanisms.  ...  Work by A.E. and D.H. has been supported in part by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University.  ... 
doi:10.1093/bioinformatics/btl325 pmid:17237094 fatcat:5r7zmdlswfc4vb74p7oxmgbeoa

Specificity in Computational Protein Design

James J. Havranek
2010 Journal of Biological Chemistry  
One motivation is to harness the exquisite functional capabilities of proteins for our own purposes.  ...  The extent of similarity between designed and natural proteins also reports on how faithfully our models represent the selective pressures that determine protein sequences.  ...  A second area of recent activity with implications for protein design is the treatment of protein backbone flexibility.  ... 
doi:10.1074/jbc.r110.157685 pmid:20670934 pmcid:PMC2951182 fatcat:zm7aecc4d5buxbwxd6lutv65d4

Encoding molecular motions in voxel maps

J. Cortes, S. Barbe, M. Erard, T. Simeon
2009 2009 IEEE International Conference on Robotics and Automation  
This paper builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool  ...  ACKNOWLEDGMENTS The authors thank Maurice Franssen, David Guieysse and Magali Remaud for providing models and information about CALB.  ...  This work has been partially supported by the Région Midi-Pyrénées under projets ITAV ALMA and CTP AMOBIO, and by the French National Agency for Research (ANR) under project NanoBioMod.  ... 
doi:10.1109/robot.2009.5152248 dblp:conf/icra/CortesBES09 fatcat:ijzk4eq3pfhwtdviecxkg6s72a

Encoding Molecular Motions in Voxel Maps

J Cortés, S Barbe, M Erard, T Siméon
2011 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
This paper builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool  ...  ACKNOWLEDGMENTS The authors thank Maurice Franssen, David Guieysse and Magali Remaud for providing models and information about CALB.  ...  This work has been partially supported by the Région Midi-Pyrénées under projets ITAV ALMA and CTP AMOBIO, and by the French National Agency for Research (ANR) under project NanoBioMod.  ... 
doi:10.1109/tcbb.2010.23 pmid:20421686 fatcat:qrzew5l4mjgepppg4ledife7jy

Equilibrium and kinetics at the coil-to-globule transition of star and comb heteropolymers in infinitely dilute solutions [article]

E.G. Timoshenko, Yu.A. Kuznetsov
2001 arXiv   pre-print
It is interesting to note that star-like conformations naturally appear for a comb polymer with a strongly hydrophobic backbone.  ...  Particular examples of combs with hydrophobic backbone and hydrophilic side-groups (and vice versa), as well as stars with flexible and semi-stiff arms are studied.  ...  We also acknowledge the support of the Centre for High Performance Computing Applications, UCD.  ... 
arXiv:cond-mat/0103102v1 fatcat:ij3bdc3de5fv7onpj5zxkgd5bq

A path planning approach for computing large-amplitude motions of flexible molecules

J. Cortes, T. Simeon, V. Ruiz de Angulo, D. Guieysse, M. Remaud-Simeon, V. Tran
2005 Bioinformatics  
Results: Two kinds of large-amplitude motion are treated in this paper: protein loop conformational changes (involving protein backbone flexibility) and ligand trajectories to deep active sites in proteins  ...  (involving ligand and protein side-chain flexibility).  ...  Protein flexibility, which plays an important role in proteinligand interactions however, is considered for protein folding applications using simplified models such as articulated backbone with bounding  ... 
doi:10.1093/bioinformatics/bti1017 pmid:15961448 fatcat:4tmbfohsqbceth5y72fvfv3g6y

Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method

Juan Cortés, Duc Thanh Le, Romain Iehl, Thierry Siméon
2010 Physical Chemistry, Chemical Physics - PCCP  
In this paper, the problem is formulated as a mechanical disassembly problem where the protein and the ligand are modeled like articulated mechanisms, and an efficient method for computing molecular disassembly  ...  Simulating protein conformational changes induced or required by the internal diffusion of a ligand is important for the understanding of their interaction mechanisms.  ...  Acknowledgments This work has been partially supported by the French National Agency for Research (ANR) under project GlucoDesign, and by the Région Midi-Pyrénées under project Amylo.  ... 
doi:10.1039/c002811h pmid:20526495 fatcat:iw4imb67xbeiziopfi7laghenq

SIMS: A Hybrid Method for Rapid Conformational Analysis

Bryant Gipson, Mark Moll, Lydia E. Kavraki, Chandra Verma
2013 PLoS ONE  
For all cases we provide energetic validations using well-established energy fields, demonstrating this framework as a fast and accurate tool for the analysis of a wide range of protein flexibility problems  ...  This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library.  ...  extensive library of protocols for protein modeling.  ... 
doi:10.1371/journal.pone.0068826 pmid:23935893 pmcid:PMC3720858 fatcat:52e4pkprgbfhxcpdwnz23o5zky

What drives the clustering of membrane-bound Ras?

Zhenlong Li, Alemayehu A. Gorfe
2012 Small GTPases  
We found that the specific nature of the lipid modification is less important for cluster formation, but plays a key role for the domain-specific distribution of the nanoclusters.  ...  Here, we provide additional details on the interplay between bilayer structure perturbation and peptide-peptide association that provide the physical driving force for clustering.  ...  This is highlighted by the expansion of the tH backbone during the simulations (Fig. 2B) .  ... 
doi:10.4161/sgtp.21829 pmid:22935734 pmcid:PMC3520890 fatcat:7kogyv4jgvf2jggsp5sxapa3za

OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features [article]

Mark A. Hallen, Jeffrey W. Martin, Adegoke Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou (+2 others)
2018 bioRxiv   pre-print
Like previous versions of OSPREY, OSPREY 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design  ...  and model conformational entropy.  ...  In Ref. 20 , we have shown that backbone flexibility as modeled by CATS is sometimes critical for avoiding nonphysical steric clashes (Fig. 7B ,C) and often affects energetics significantly.  ... 
doi:10.1101/306324 fatcat:cnbgcsf6mjeltmcr7yjg3q7lni

Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization

Anna S. Kamenik, Uta Lessel, Julian E. Fuchs, Thomas Fox, Klaus R. Liedl
2018 Journal of Chemical Information and Modeling  
By applying an energetic cutoff, followed by geometric clustering, we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic  ...  Using three different model systems of varying size and flexibility, we show that the method reliably reproduces experimentally determined structural ensembles and is capable of identifying key conformational  ...  (Pro-Serleu-Asp-Val), starting conformations were constructed based on published backbone torsions using the "Protein Builder" tool in MOE.  ... 
doi:10.1021/acs.jcim.8b00097 pmid:29652495 pmcid:PMC5974701 fatcat:oah3p6znfvgifclcnczr3rfrq4

Seeking allosteric networks in PDZ domains

Candice Gautier, Louise Laursen, Per Jemth, Stefano Gianni
2018 Protein Engineering Design & Selection  
In this review, we first describe theoretical and experimental approaches that were used to probe the energetic network(s) in PDZ domains.  ...  residues in the postsynaptic density-95/Discs large/Zonula occludens 1 (PDZ) domain family to a statistical correlation analysis, PDZ domains have represented a paradigmatic family to explore single domain protein  ...  Based on the results, they proposed a general thermodynamic allosteric network for the PDZ family in which three clusters of residues energetically coupled to H372 were identified; the first cluster is  ... 
doi:10.1093/protein/gzy033 pmid:30690500 pmcid:PMC6508479 fatcat:5o2qjudkfbdozpprrnqomy4p4y
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