scholarly journals The set of realizations of a max-plus linear sequence is semi-polyhedral

2011 ◽  
Vol 77 (4) ◽  
pp. 820-833 ◽  
Author(s):  
Vincent Blondel ◽  
Stéphane Gaubert ◽  
Natacha Portier
Keyword(s):  
Linear Sequence

The Total Synthesis of Rhabdastrellic Acid A

2018 ◽  
Author(s):  
Yaroslav Boyko ◽  
Christopher Huck ◽  
David Sarlah
Keyword(s):  
Total Synthesis ◽  
Late Stage ◽  
Cross Coupling ◽  
Side Chains ◽  
General Strategy ◽  
Modular Approach ◽  
Linear Sequence ◽  
Generating Sequence ◽  
First Time

<div>The first total synthesis of rhabdastrellic acid A, a highly cytotoxic isomalabaricane triterpenoid, has been accomplished in a linear sequence of 14 steps from commercial geranylacetone. The prominently strained <i>trans-syn-trans</i>-perhydrobenz[<i>e</i>]indene core characteristic of the isomalabaricanes is efficiently accessed in a selective manner for the first time through a rapid, complexity-generating sequence incorporating a reductive radical polyene cyclization, an unprecedented oxidative Rautenstrauch cycloisomerization, and umpolung 𝛼-substitution of a <i>p</i>-toluenesulfonylhydrazone with in situ reductive transposition. A late-stage cross-coupling in concert with a modular approach to polyunsaturated side chains renders this a general strategy for the synthesis of numerous family members of these synthetically challenging and hitherto inaccessible marine triterpenoids.</div>

scholarly journals A new classification and linear sequence of extant gymnosperms

Phytotaxa ◽  
2011 ◽  
Vol 19 (1) ◽  
pp. 55 ◽  
Author(s):  
M. J. M. Christenhusz ◽  
J. L. Reveal ◽  
A. Farjon ◽  
M. F. Gardner ◽  
R. R. Mill ◽  
...  
Keyword(s):  
New Classification ◽  
Linear Sequence

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

scholarly journals Structure and function relationships of proteins based on polar profile: a review.

2016 ◽  
Vol 63 (2) ◽  
Author(s):  
Carlos Polanco ◽  
Thomas Buhse ◽  
Vladimir N Uversky
Keyword(s):  
Mathematical Structure ◽  
Quantitative Structure Activity Relationship ◽  
Multidrug Resistant ◽  
Training Data ◽  
Main Function ◽  
Pharmaceutical Drugs ◽  
Linear Sequence ◽  
Wide Range ◽  
High Level ◽  
And Function

Proteins in the post-genome era impose diverse research challenges, the main are the understanding of their structure-function mechanism, and the growing need for new pharmaceutical drugs, particularly antibiotics that help clinicians treat the ever- increasing number of Multidrug-Resistant Organisms (MDROs). Although, there is a wide range of mathematical-computational algorithms to satisfy the demand, among them the Quantitative Structure-Activity Relationship algorithms that have shown better performance using a characteristic training data of the property searched; their performance has stagnated regardless of the number of metrics they evaluate and their complexity. This article reviews the characteristics of these metrics, and the need to reconsider the mathematical structure that expresses them, directing their design to a more comprehensive algebraic structure. It also shows how the main function of a protein can be determined by measuring the polarity of its linear sequence, with a high level of accuracy, and how such exhaustive metric stands as a "fingerprint" that can be applied to scan the protein regions to obtain new pharmaceutical drugs, and thus to establish how the singularities led to the specialization of the protein groups known today.

scholarly journals Sentence Generation for Entity Description with Content-Plan Attention

2020 ◽  
Vol 34 (05) ◽  
pp. 9057-9064
Author(s):  
Bayu Trisedya ◽  
Jianzhong Qi ◽  
Rui Zhang
Keyword(s):  
State Of The Art ◽  
Neural Models ◽  
Time Step ◽  
Two Stage ◽  
Sentence Generation ◽  
Neural Data ◽  
Attention Model ◽  
Linear Sequence ◽  
Proper Order ◽  
Real World Datasets

We study neural data-to-text generation. Specifically, we consider a target entity that is associated with a set of attributes. We aim to generate a sentence to describe the target entity. Previous studies use encoder-decoder frameworks where the encoder treats the input as a linear sequence and uses LSTM to encode the sequence. However, linearizing a set of attributes may not yield the proper order of the attributes, and hence leads the encoder to produce an improper context to generate a description. To handle disordered input, recent studies propose two-stage neural models that use pointer networks to generate a content-plan (i.e., content-planner) and use the content-plan as input for an encoder-decoder model (i.e., text generator). However, in two-stage models, the content-planner may yield an incomplete content-plan, due to missing one or more salient attributes in the generated content-plan. This will in turn cause the text generator to generate an incomplete description. To address these problems, we propose a novel attention model that exploits content-plan to highlight salient attributes in a proper order. The challenge of integrating a content-plan in the attention model of an encoder-decoder framework is to align the content-plan and the generated description. We handle this problem by devising a coverage mechanism to track the extent to which the content-plan is exposed in the previous decoding time-step, and hence it helps our proposed attention model select the attributes to be mentioned in the description in a proper order. Experimental results show that our model outperforms state-of-the-art baselines by up to 3% and 5% in terms of BLEU score on two real-world datasets, respectively.

scholarly journals Total Synthesis of the Reported Structure of Cahuitamycin A

2020 ◽  
Author(s):  
Justin Shapiro ◽  
Savannah Post ◽  
William Wuest
Keyword(s):  
Natural Products ◽  
Total Synthesis ◽  
Natural Product ◽  
Twelve Step ◽  
Target Compound ◽  
New Family ◽  
Iron Trafficking ◽  
Linear Sequence ◽  
Alternative Structure ◽  
Synthetic Target

In a 2016 screen of natural product extracts a new family of natural products, the cahuitamycins, was discovered and found to inhibit the formation of biofilms in the human pathogen <i>Acinetobacter baumannii</i>. The molecules contain an unusual piperazate residue that raises structure/function and biosynthesis questions and resemble iron-trafficking virulence factors from <i>A. baumannii</i>, suggesting a connection between metal homeostasis and biofilm-mediated pathogenicity. Here we disclose the first total synthesis of the reported structure of cahuitamycin A in a twelve-step longest linear sequence and 18% overall yield. Comparison of spectral data of the authentic natural product and synthetic target compound demonstrate that the reported structure is distinct from the isolated metabolite. Herein, we propose an alternative structure to reconcile our findings with the isolation report, setting the stage for future synthetic and biochemical investigations of an important class of natural products.

scholarly journals DNA energy constraints shape biological evolutionary trajectories

2019 ◽  
Author(s):  
Piero Fariselli ◽  
Cristian Taccioli ◽  
Luca Pagani ◽  
Amos Maritan
Keyword(s):  
Dna Sequence ◽  
Double Helix ◽  
Maximum Entropy Principle ◽  
Biological Information ◽  
Human Populations ◽  
Dsdna Molecule ◽  
Linear Sequence ◽  
Energy Constraints ◽  
Entropy Principle ◽  
Evolutionary Trajectories

AbstractMost living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetrate themselves. Thus, the biological information contained within a dsDNA molecule, in terms of a linear sequence of nucleotides, has been considered the main target of the evolution. However, in this information-centred perspective, certain DNA sequence symmetries are difficult to explain. Here we show that these patterns can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. Our predictions are valid for both prokaryotes and eukaryotes, and also inform the interpretation of observed codon biases and context-dependent mutation patterns in human populations. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the biological selective processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.

scholarly journals Explorations in Parallel  Linear Genetic Programming

2021 ◽  
Author(s):  
◽  
Carlton Downey
Keyword(s):  
Genetic Programming ◽  
Convergence Time ◽  
Linear Genetic Programming ◽  
Cooperative Coevolution ◽  
Biological Inspiration ◽  
Linear Sequence ◽  
New Form ◽  
Program Output ◽  
Program Components ◽  
Crossover And Mutation

<p>Linear Genetic Programming (LGP) is a powerful problem-solving technique, but one with several significant weaknesses. LGP programs consist of a linear sequence of instructions, where each instruction may reuse previously computed results. This structure makes LGP programs compact and powerful, however it also introduces the problem of instruction dependencies. The notion of instruction dependencies expresses the concept that certain instructions rely on other instructions. Instruction dependencies are often disrupted during crossover or mutation when one or more instructions undergo modification. This disruption can cause disproportionately large changes in program output resulting in non-viable offspring and poor algorithm performance. Motivated by biological inspiration and the issue of code disruption, we develop a new form of LGP called Parallel LGP (PLGP). PLGP programs consist of n lists of instructions. These lists are executed in parallel, and the resulting vectors are summed to produce the overall program output. PLGP limits the disruptive effects of crossover and mutation, which allows PLGP to significantly outperform regular LGP. We examine the PLGP architecture and determine that large PLGP programs can be slow to converge. To improve the convergence time of large PLGP programs we develop a new form of PLGP called Cooperative Coevolution PLGP (CC PLGP). CC PLGP adapts the concept of cooperative coevolution to the PLGP architecture. CC PLGP optimizes all program components in parallel, allowing CC PLGP to converge significantly faster than conventional PLGP. We examine the CC PLGP architecture and determine that performance</p>

scholarly journals Structural basis for UFM1 transfer from UBA5 to UFC1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Manoj Kumar ◽  
Prasanth Padala ◽  
Jamal Fahoum ◽  
Fouad Hassouna ◽  
Tomer Tsaban ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Structural Basis ◽  
Adenylation Domain ◽  
Post Translational Modification ◽  
Target Proteins ◽  
Cellular Processes ◽  
Enzyme Cascade ◽  
Linear Sequence ◽  
C Terminus

AbstractUfmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1’s active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1’s conjugation machinery and may serve as a basis for the development of ufmylation inhibitors.

Sign in / Sign up

Export Citation Format

Share Document