Pinboard (Vaguery) https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery Site-saturation mutagenesis of 500 human protein domains | Nature 2025-04-12T13:22:20+00:00 https://www.nature.com/articles/s41586-024-08370-4 Vaguery structural-biology biochemistry molecular-biology impressive looking-to-see neural-networks protein-folding to-write-about evolutionary-biology variation-as-a-source-of-innovation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:604c7c235a9a/ Some Proteins Change Their Folds to Perform Different Jobs | Quanta Magazine 2022-01-20T16:29:55+00:00 https://www.quantamagazine.org/metamorphic-proteins-change-their-folds-for-different-jobs-20210203/ Vaguery structural-biology protein-folding biological-engineering multitask-learning rather-interesting examples https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b97926810368/ Predicting improved protein conformations with a temporal deep recurrent neural network | bioRxiv 2021-06-04T11:19:21+00:00 https://www.biorxiv.org/content/10.1101/275008v1?rss=1 Vaguery protein-folding structural-biology machine-learning recurrent-neural-network deep-learning rather-interesting dynamical-systems to-simulate to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:82ac88eb634f/ [0706.1754] Protein structure prediction by an iterative search method 2020-01-14T21:41:45+00:00 https://arxiv.org/abs/0706.1754 Vaguery protein-folding heuristics hill-climbing rather-interesting metaheuristics old to-write-about to-simulate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a9a0f4f2c4d9/ [1610.07277] Rapid calculation of side chain packing and free energy with applications to protein molecular dynamics 2017-10-12T10:56:57+00:00 https://arxiv.org/abs/1610.07277 Vaguery structural-biology approximation heuristics algorithms protein-folding to-write-about nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:afdc2b1f0a08/ [1608.06971] Protein Collapse is Encoded in the Folded State Architecture 2016-12-31T11:50:08+00:00 https://arxiv.org/abs/1608.06971 Vaguery structural-biology protein-folding rather-interesting bioinformatics theoretical-biology self-organization engineering-design dynamical-systems https://pinboard.in/ https://pinboard.in/u:Vaguery/b:81ce4c9f7934/ [1511.00139] Chaos of Protein Folding 2016-03-26T20:51:51+00:00 http://arxiv.org/abs/1511.00139 Vaguery protein-folding Devaney-Model theoretical-biology structural-biology nudge-targets consider:representation consider:looking-to-see metaheuristics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:01bc08b528b6/ [1501.03971] Bayesian protein structure alignment 2016-02-27T21:43:28+00:00 http://arxiv.org/abs/1501.03971 Vaguery biochemistry structural-biology protein-folding bioinformatics algorithms machine-learning statistics metrics nudge-targets consider:distance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:eefeff02cf1a/ [1601.03420] Critical fluctuations in proteins native states 2016-02-24T23:37:17+00:00 http://arxiv.org/abs/1601.03420 Vaguery biophysics protein-folding physics phase-transitions self-organization looking-to-see nonlinear-dynamics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:71906633e624/ [1509.03434] Improving protein threading accuracy via combining local and global potential using TreeCRF model 2015-12-25T17:11:31+00:00 http://arxiv.org/abs/1509.03434 Vaguery structural-biology biophysics protein-folding models optimization algorithms representation nudge-targets bioinformatics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ad99a83404f6/ [1505.05709] A Conformational Search Method for Protein Systems Using Genetic Crossover and Metropolis Criterion 2015-05-26T10:59:20+00:00 http://arxiv.org/abs/1505.05709 Vaguery metaheuristics protein-folding energy-landscapes nudge-targets simulation meh? https://pinboard.in/ https://pinboard.in/u:Vaguery/b:1be80c6869cf/ [1410.4465] On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment 2015-03-15T20:39:42+00:00 http://arxiv.org/abs/1410.4465 Vaguery bioinformatics biochemistry structural-biology protein-folding Thom-LaBean's-thesis it's-more-complicated-than-you-think Oh Science. https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e941d1fa5934/ [1310.5091] Synchronization as a unifying mechanism for protein folding 2014-11-09T12:21:24+00:00 http://arxiv.org/abs/1310.5091 Vaguery protein-folding molecular-design coupled-oscillators simulation coordination rather-interesting nudge-targets consider:detectors https://pinboard.in/ https://pinboard.in/u:Vaguery/b:32a42af2d6c6/ [1409.3397] Are there Unfoldable Proteins in Dimension Three? 2014-09-24T11:03:41+00:00 http://arxiv.org/abs/1409.3397 Vaguery protein-folding Dill-models biophysics simulation abstraction proof-of-concept nudge-targets foldability biological-engineering consider:performance-criteria https://pinboard.in/ https://pinboard.in/u:Vaguery/b:73326b64d2ed/ [1311.1301] Prediction of residue-residue contacts from protein families using similarity kernels and least squares regularization 2014-04-07T12:06:37+00:00 http://arxiv.org/abs/1311.1301 Vaguery protein-folding machine-learning partial-solutions prediction nudge-targets consider:more details https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a5f9740f8e49/ [1312.0867] Frustration in Biomolecules 2014-03-30T11:28:16+00:00 http://arxiv.org/abs/1312.0867 Vaguery protein-folding energy-landscapes biophysics simulation entropy complexology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:83b56a9e9f3a/ [1310.1403] Sequence-Structure Relationship in Proteins: a Computational Analysis of Proteins that Differ in Sequence but Share the Same Fold 2013-11-16T19:56:16+00:00 http://arxiv.org/abs/1310.1403 Vaguery structural-biology protein-folding biological-engineering biophysics interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f6a4059c8d99/ [1309.7694] Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles 2013-10-06T13:20:50+00:00 http://arxiv.org/abs/1309.7694 Vaguery SOMs protein-folding structural-biology biophysics metaheuristics feature-extraction clustering https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cdf3f860bb4c/ [1306.2852] Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space 2013-06-17T12:28:07+00:00 http://arxiv.org/abs/1306.2852 Vaguery structural-biology protein-folding energy-landscapes algorithms heuristics tiling interesting nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:118950cd383b/ [1207.6431] Optimal reconstruction of the folding landscape using differential energy surface analysis 2013-05-25T11:10:38+00:00 http://arxiv.org/abs/1207.6431 Vaguery biochemistry protein-folding fitness-landscapes nudge-targets algorithms performance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:33b681fa8b38/ [1304.7241] pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study 2013-04-30T21:56:20+00:00 http://arxiv.org/abs/1304.7241 Vaguery biochemistry protein-folding structural-biology engineering-design biological-engineering nudge-targets simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8e7ba4a2acc9/ [1212.4312] pH-dependent coarse-grained model of peptides 2013-04-30T21:55:33+00:00 http://arxiv.org/abs/1212.4312 Vaguery structural-biology protein-folding biochemistry models simulation interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8d8919003693/ [1303.6231] From mechanical folding trajectories to intrinsic energy landscapes of biopolymers 2013-04-21T15:09:06+00:00 http://arxiv.org/abs/1303.6231 Vaguery structural-biology biological-engineering experiment energy-landscapes protein-folding https://pinboard.in/ https://pinboard.in/u:Vaguery/b:651b230099ee/ [1303.3898] Crumpled globule possesses the properties of molecular machines 2013-03-30T14:09:53+00:00 http://arxiv.org/abs/1303.3898 Vaguery molecular-design molecular-machinery structural-biology energy-landscapes protein-folding nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d43fda22c6ea/ [1211.0662] Hidden Complexity in the Isomerization Dynamics of Holliday Junctions 2013-03-06T19:06:36+00:00 http://arxiv.org/abs/1211.0662 Vaguery molecular-design molecular-machinery biochemistry experiment protein-folding structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:95b009c64a0f/ [1206.6332] Characterizing protein crystal contacts and their role in protein crystallization 2012-08-29T12:33:03+00:00 http://arxiv.org/abs/1206.6332 Vaguery protein-folding simulation experiment meta-modeling nudge-targets proxy-modeling https://pinboard.in/ https://pinboard.in/u:Vaguery/b:77b055aa8367/ [1102.5694] Evolutionary Dynamics in a Simple Model of Self-Assembly 2011-04-02T12:11:10+00:00 http://arxiv.org/abs/1102.5694 Vaguery self-assembly genetic-programming genetic-algorithm nanotechnology complexology protein-folding nudge-targets https://pinboard.in/u:Vaguery/b:504e3efd868b/ Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model 2008-01-06T14:45:38+00:00 http://precedings.nature.com/documents/1490/version/1 Vaguery protein-folding crystallography machine-learning pattern-discovery data-mining bioinformatics structural-biology https://pinboard.in/u:Vaguery/b:aee500c2adfa/