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Diffraction is the most common method to solve for unknown or partially known crystal structures. However, it remains a challenge to determine the crystal structure of a new material that may have nanoscale size or heterogeneities. Here we…

Artificial intelligence (AI) in the form of deep learning bears promise for drug discovery and chemical biology, $\textit{e.g.}$, to predict protein structure and molecular bioactivity, plan organic synthesis, and design molecules…

生物大分子 · 定量生物学 2022-12-29 Rıza Özçelik , Derek van Tilborg , José Jiménez-Luna , Francesca Grisoni

Protein Structure Predication from sequences of amino acid has gained a remarkable attention in recent years. Even though there are some prediction techniques addressing this problem, the approximate accuracy in predicting the protein…

计算工程、金融与科学 · 计算机科学 2014-01-14 Pokkuluri Kiran Sree , Inamupudi Ramesh Babu , SSSN Usha Devi N

Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…

计算机视觉与模式识别 · 计算机科学 2020-09-01 Alexander Hudson , Shaogang Gong

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one…

生物大分子 · 定量生物学 2016-08-02 Irem Altan , Patrick Charbonneau , Edward H. Snell

One of the long-standing problems in materials science is how to predict a material's structure and then its properties given only its composition. Experimental characterization of crystal structures has been widely used for structure…

材料科学 · 物理学 2022-03-29 Rongzhi Dong , Yong Zhao , Yuqi Song , Nihang Fu , Sadman Sadeed Omee , Sourin Dey , Qinyang Li , Lai Wei , Jianjun Hu

Chemical imaging provides information about the distribution of chemicals within a target. When combined with structural information about the target, in situ chemical imaging opens the door to applications ranging from tissue…

图像与视频处理 · 电气工程与系统科学 2020-12-02 Luke Pfister , Rohit Bhargava , Yoram Bresler , P. Scott Carney

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry.…

机器学习 · 计算机科学 2024-01-31 Shengchao Liu , Weili Nie , Chengpeng Wang , Jiarui Lu , Zhuoran Qiao , Ling Liu , Jian Tang , Chaowei Xiao , Anima Anandkumar

Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…

软凝聚态物质 · 物理学 2012-01-18 Aaron S. Keys , Christopher R. Iacovella , Sharon C. Glotzer

Discovery of the molecular candidates for applications in drug targets, biomolecular systems, catalysts, photovoltaics, organic electronics, and batteries, necessitates development of machine learning algorithms capable of rapid exploration…

机器学习 · 计算机科学 2023-12-12 Ayana Ghosh , Sergei V. Kalinin , Maxim A. Ziatdinov

Databases of gas and surface chemical reactions are a key tool for scientists working in a wide range of physical sciences. In Astrochemistry, databases of chemical reactions are used as inputs to chemical models to determine the abundances…

星系天体物理 · 物理学 2021-01-14 Serena Viti , Jonathan Holdship

High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry…

机器学习 · 统计学 2017-09-29 Ivo D. Shterev , David B. Dunson , Cliburn Chan , Gregory D. Sempowski

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…

生物大分子 · 定量生物学 2013-02-01 Pablo Cordero , Wipapat Kladwang , Christopher C. VanLang , Rhiju Das

Rapid and reliable detection and identification of unknown chemical substances is critical to homeland security. It is challenging to identify chemical components from a wide range of explosives. There are two key steps involved. One is a…

数值分析 · 数学 2011-10-10 Y. Sun , J. Xin

Determining the structure and following the structural evolution of molecules undergoing chemical reactions is one of the key goals of ultrafast molecular physics and chemistry. Recently, Coulomb explosion imaging has emerged as a promising…

A long-standing goal of science is to accurately solve the Schr\"odinger equation for large molecular systems. The poor scaling of current quantum chemistry algorithms on classical computers imposes an effective limit of about a few dozen…

化学物理 · 物理学 2022-02-11 Joshua A. Rackers , Lucas Tecot , Mario Geiger , Tess E. Smidt

Machine learning can reveal new insights into X-ray spectroscopy of liquids when the local atomistic environment is presented to the model in a suitable way. Many unique structural descriptor families have been developed for this purpose.…

化学物理 · 物理学 2024-08-26 E. A. Eronen , A. Vladyka , Ch. J. Sahle , J. Niskanen

Predicting the chemical properties of compounds is crucial in discovering novel materials and drugs with specific desired characteristics. Recent significant advances in machine learning technologies have enabled automatic predictive…

定量方法 · 定量生物学 2021-12-10 Yang Liu , Hisashi Kashima

Symmetry plays a major role in subgraph matching both in the description of the graphs in question and in how it confounds the search process. This work addresses how to quantify these effects and how to use symmetries to increase the…

数据结构与算法 · 计算机科学 2023-01-10 Dominic Yang , Yurun Ge , Thien Nguyen , Jacob Moorman , Denali Molitor , Andrea Bertozzi

A key challenge in automated chemical compound space explorations is ensuring veracity in minimum energy geometries---to preserve intended bonding connectivities. We discuss an iterative high-throughput workflow for connectivity preserving…

化学物理 · 物理学 2020-10-16 Salini Senthil , Sabyasachi Chakraborty , Raghunathan Ramakrishnan