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RNA结构预测
文章平均质量分 84
给定RNA序列,预测RNA二级或三级结构
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JTVAE( Junction Tree Variational Autoencoder )
Junction Tree Variational Autoencoder for Molecular Graph GenerationYear: 2018Authors: Wengong Jin, Regina Barzilay, Tommi JaakkolaJournal Name: ICMLInnovation原创 2022-04-10 10:00:55 · 1800 阅读 · 0 评论 -
De Novo Prediction of RNA 3D Structures with Deep Learning
De Novo Prediction of RNA 3D Structures with Deep LearningYear: 2022Authors: Julius Ramakers, Christopher Frederik Blum, Sabrina K¨onig, Stefan Harmeling, Markus KollmannJournal Name: bioxiv1 Innovation结合自回归深度生成模型、蒙特卡罗树搜索和分数模型预测 RNA 三维折叠结构。2 Method原创 2022-03-12 11:35:05 · 1943 阅读 · 0 评论 -
PINN potentials
Physically informed artificial neural networks for atomistic modeling of materialsYear: 2019Authors: G. P. Purja Pun, R. Batra, R. Ramprasad & Y. MishinJournal Name: Nature CommunicationsInnovation扩展物理模型,使其具有广泛适用性,即在训练集覆盖不到的数据中也能适用。引入与局部结构参数 Gil原创 2022-02-17 13:31:45 · 409 阅读 · 0 评论 -
RNAcmap--predicting contact maps of RNAs by evolutionary coupling analysis
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysisYear: 2021Authors: Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip Paliwal and Yaoqi ZhouJournal Name: BioinformaticsMotivation原创 2022-01-26 15:42:29 · 363 阅读 · 0 评论 -
ARES( Atomic Rotationally Equivariant Scorer )
Geometric deep learning of RNA structureYear: 2021Authors: Raphael J. L. Townshend, Stephan Eismann, Andrew M. Watkins, Ramya Rangan, Maria Karelina, Rhiju Das, Ron O. DrorJournal Name: ScienceDatasetBackgroundMethodEquivariant convolution等变卷积基于滤波原创 2022-01-24 16:13:32 · 450 阅读 · 0 评论 -
BLAST
Basic Local Alignment Search ToolYear: 1990Authors: Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers and David J. LipmanJournal Name: Journal of Molecular BiologyAbstract一个快速进行序列比较的新方法:基本局部比对搜索工具( basic local alignment search tool, BLAST原创 2021-11-24 19:40:05 · 215 阅读 · 0 评论 -
LinearPartition
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilitiesYear: 2020Authors: He Zhang, Liang Zhang, David H. Mathews and Liang HuangJournal Name: BioinformaticsMotivation传统分割方法的复杂度与序列长度呈三次方关系。Research原创 2021-11-22 21:39:35 · 649 阅读 · 0 评论 -
SPOT-RNA
RNA secondary structure prediction using stochastic context-free grammars and evolutionary historyYear: 1999Authors: B. Knudsen and J. HeinJournal Name: BioinformaticsMotivation最近,一些进化模型被应用于结构预测中,这些模型忽略了一些相关信息。什么叫进化模型?什么样的相关信息?Research Objective结合 s原创 2021-11-10 16:51:34 · 920 阅读 · 0 评论 -
SCFGs
Stochastic context-free grammars for tRNA modelingYear: 1994Authors: Yasubumi Sakakibara, Michael Brown, Richard Hughey, I.Saira Mian, Kimmen Sjolander, Rebecca C.Underwood and David HausslerJournal Name: Nucleic Acids ResearchResearch Objective通过类似于构原创 2021-11-09 13:52:46 · 368 阅读 · 0 评论 -
MXfold2
RNA secondary structure prediction using deep learning with thermodynamic integrationYear: 2021Authors: Kengo Sato, Manato Akiyama & Yasubumi SakakibaraJournal Name: Nature CommunicationsMotivation在多参数模型种经常会出现过拟合现象Research Objective实现一种更具鲁棒性的结构预原创 2021-11-07 21:16:50 · 397 阅读 · 0 评论 -
Loss-augmented Max-margin Constraint Generation(LAM-CG) algorithm
Computational approaches for RNA energy parameter estimationYear: 2010Authors: MIRELA ANDRONESCU, ANNE CONDON, HOLGER H. HOOS, DAVID H. MATHEWS, and KEVIN P. MURPHYJournal Name: BIOINFORMATICSMotivation将最大间隔应用于CG模型中Research Objective改进估计能量参数的优化方法。B原创 2021-11-06 20:51:21 · 115 阅读 · 0 评论 -
Dynamic programming algorithm
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationYear: 1981Authors: Michael Zuker and Patrick StieglerJournal Name: Nucleic Acids ResearchMotivation将动态规划算法与热动力学数据结合。Research Objective基于动态规划算法提出一种更有效、快速、并且原创 2021-11-06 14:37:09 · 318 阅读 · 0 评论 -
Constraint generation(CG) approach
Efficient parameter estimation for RNA secondary structure predictionYear: 2007Authors: Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, and Kevin P. MurphyJournal Name: BioinformaticsMotivation基于自由能的RNA二级序列预测模型Turner99,没有有效、快速的参数估计方原创 2021-11-05 16:15:27 · 147 阅读 · 0 评论