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7 Computational protein design and discovery
2004
Annual Reports Section C (Physical Chemistry)
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As many of these forces are subtle and their simultaneous optimization is a problem of great complexity, sophisticated sequence prediction algorithms have been developed to aid in the design of novel proteins ...
to a large-scale design of de novo proteins. ...
S. is a Cottrell Scholar of Research Corporation and an Arnold and Mabel Beckman Foundation Young Investigator. ...
doi:10.1039/b313669h
fatcat:4v7kua5e75hu3ke2ogp5zka4ua
An algorithm to parse segment packing in predicted protein contact maps
2016
Algorithms for Molecular Biology
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For the larger protein, this involved examples of the algorithm apportioning parts of a single large secondary structure element between two different interactions. ...
The method was shown to be effective when applied to the transmembrane class of protein and error tolerant even when the signal becomes degraded. ...
Availability of data and materials All data and program souce codes can be found in the Supplementary Material associated with this paper. ...
doi:10.1186/s13015-016-0080-x
pmid:27330543
pmcid:PMC4912788
fatcat:zzqnriogrzcgpjbariggukupei
Learning the Language of Biological Sequences
[chapter]
2016
Topics in Grammatical Inference
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, it is still a source of open and nice inspirational problems for grammatical inference, enabling us to confront our ideas to real fundamental applications. ...
Learning the language of biological sequences is an appealing challenge for the grammatical inference research field. ...
proteins [96] and transmembrane regions in proteins [97] , whose performances are close to those of dedicated tools built with human expertise. ...
doi:10.1007/978-3-662-48395-4_8
fatcat:eojckskf65f5phcbmjsfbq7era
Artificial intelligence and molecular biology
1994
ChoiceReviews
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See [Baddeley, 1986] for an overview of algorithms for two-dimensional segmentation. ...
For a detailed description of the frame representation for imagery and the implementation of the depict function see [Papadias 1990 ]. 2. ...
of the folded protein. ...
doi:10.5860/choice.31-3826
fatcat:5jmryy7mkbcrvifz6ahlbbdceu
Current Progress in Static and Dynamic Modeling of Biological Networks
[chapter]
2010
Systems Biology for Signaling Networks
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In this review we discuss techniques for both of these modeling paradigms, illustrating each by reference to important recent papers. ...
This first step in this process is reconstructing molecular anatomy through static modeling, the determination of which pieces (DNA, RNA, protein, and metabolite) is present, and how they are related ( ...
Acknowledgements We thank Russ Altman for helpful discussions. ...
doi:10.1007/978-1-4419-5797-9_2
fatcat:7pwcze2sbraszfcy5yacypur7e
Transition path sampling and forward flux sampling. Applications to biological systems
2009
Journal of Physics: Condensed Matter
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folding, and enzyme catalysis. ...
While path sampling methods have a widespread application to many types of rare transitional events, here only recent applications involving biomolecules are reviewed, including isomerizations, protein ...
Bolhuis for allowing us to modify their picture files. ...
doi:10.1088/0953-8984/21/33/333101
pmid:21828593
fatcat:zhovbj6frjcvrnd75674x3z47i
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs
[chapter]
2011
Lecture Notes in Computer Science
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Using our motif-based predictions we were also able to correct annotation errors in public databases for the location of some of the proteins. ...
Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. ...
DME (Discriminative Matrix Enumerator) [49] uses a different approach for discriminative learning of a PWM. A global, enumerative search on a discrete space of PWM. ...
doi:10.1007/978-3-642-20036-6_20
fatcat:jc2zx6wmrzbzjgiczc6pcosn7e
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs
2011
Journal of Computational Biology
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Using our motif-based predictions we were also able to correct annotation errors in public databases for the location of some of the proteins. ...
Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. ...
DME (Discriminative Matrix Enumerator) [49] uses a different approach for discriminative learning of a PWM. A global, enumerative search on a discrete space of PWM. ...
doi:10.1089/cmb.2011.0193
pmid:21999284
pmcid:PMC3216107
fatcat:fzqi5tdydbgb5jkwc7oqjexjuu
Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
2009
Molecular Systems Biology
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To quantify signal flow through ErbB-activated pathways we have constructed, trained and analyzed a mass action model of immediate-early signaling involving ErbB1-4 receptors (EGFR, HER2/Neu2, ErbB3 and ...
Modeling predicts log-linear amplification so that significant ERK and Akt activation is observed at ligand concentrations far below the K d for receptor binding. ...
Acknowledgements We thank Laura Sontag-Kleiman, Julio Saez-Rodriguez and Carlos Lopez for discussion and editing and Taeshin Park for assistance with Jacobian. ...
doi:10.1038/msb.2008.74
pmid:19156131
pmcid:PMC2644173
fatcat:kkzeuupzanamhmakcdiamcl3ci
A Survey of Computational Methods for Protein Function Prediction
[chapter]
2016
Big Data Analytics in Genomics
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Here we review these methods and the state of protein function prediction, emphasizing recent algorithmic developments, remaining challenges, and prospects for future research. ...
neighbors in a protein-protein interaction network, from microarray data, or a combination of these different types of data. ...
Acknowledgements Funding for this work is provided in part by NSF-IIS1144106.
References ...
doi:10.1007/978-3-319-41279-5_7
fatcat:pejwmwpoarhyjhulevmkbavocm
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning
[article]
2020
arXiv
pre-print
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We instead propose a novel Reinforcement Learning framework for molecular design in which an agent learns to directly optimize through a space of synthetically-accessible drug-like molecules. ...
We validate our method by demonstrating that it outperforms existing state-of the art approaches in the optimization of pharmacologically-relevant objectives, while results on multi-objective optimization ...
The methods and algorithms presented here were developed at InVivo AI. ...
arXiv:2004.14308v2
fatcat:dbmnzvy3mfdl5np7hlnwsz3ama
Pathway analysis for BioAmbients
2008
The Journal of Logic and Algebraic Programming
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Systems Biology aims for a holistic understanding of biological processes. In order to make this understanding operational and testable it can be recorded into formal process calculus models. ...
This is a difficult task, however, because such formal models and their, often infinitely many, consequences are hard to enumerate and understand. ...
We model the transmembranal LDL receptors and the membrane patch that will later fold into the early endosome as a process capable of evolving into the EE ambient (lines [19] [20] [21] . ...
doi:10.1016/j.jlap.2008.05.006
fatcat:rr52l4n2bbco7m6ns3lrmtgb6a
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
[article]
2022
bioRxiv
pre-print
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responsible for adaptive rewiring. ...
Causal tracing demonstrates that this provides a sufficient quantitative explanation for initial and acquired responses to multiple different RAF and MEK inhibitors individually and in combination. ...
.), a Novartis Foundation fellowship to L.G., HFSP grant LT000259/2019-L1 to F.F.. ...
doi:10.1101/2022.02.17.480899
fatcat:2cvmttald5gppokgs3o5is2umq
Computational Methods in Drug Discovery
2013
Pharmacological Reviews
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Authorship Contributions Wrote or contributed to the writing of the manuscript: Sliwoski, Kothiwale, Meiler, Lowe. ...
Melo and Sali (2007) applied a genetic algorithm that used 21 input model features like sequence alignment scores, measures of protein packing, and geometric descriptors to assess folds of models. ...
Anton has been used successfully for full atomic resolution protein folding (Lindorff-Larsen et al., 2011) . ...
doi:10.1124/pr.112.007336
pmid:24381236
pmcid:PMC3880464
fatcat:4dzrdkspkjecnombnchznma2ny
Computational Strategies for a System-Level Understanding of Metabolism
2014
Metabolites
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To this aim, a plethora of methods have been developed, yet it is generally hard to identify which computational strategy is most suited for the investigation of a specific aspect of metabolism. ...
, especially when dealing with a shortage of experimental measurements. ...
If a gene is repressed, the fluxes of reactions involving the corresponding protein product will be constrained to zero. ...
doi:10.3390/metabo4041034
pmid:25427076
pmcid:PMC4279158
fatcat:phwvjs7sebbkpkj5i7plfkjm54
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