XueLab

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[[ workshop:timeline | Timeline ]]

====== Deep Learning ======
  * [[workshop:spotrna | Reproduction of SPOTRNA]] (by Haoren Qiu, 20240323)
  * [[workshop:pcann | Reproduction of PCANN]] (by Haocheng Sun, 20251122)
  * [[workshop:pspred | Protein Structure Prediction 1: Training of SPIRED]] (by Yuankuan Zhang, 20260117)
  * [[workshop:pspred-attention | Protein Structure Prediction 2: Algorithm of Attention]] (by Yuankuan Zhang, 20260124)

====== DFT ======
  * [[workshop:dft | DFT]] (by Yikan Zhang, 20251011)
  * [[workshop:dft-cs | DFT for chemical shift]] (by Prof. Xue, 20260131)

====== Molecular Dynamics ======
  * [[workshop:nmr_restraints | NMR restraints in amber ]] (by Lan Xiang, 20231118)
  * [[workshop:cpptraj | Introduction of CPPTARJ/PYTRAJ ]] (by Banglong Wang, 20231118)
  * [[workshop:wham | Weighted Histogram Analysis Method ]] (by Lu Yan, 20231202)
  * [[workshop:modified_residue | Modified residued in Amber ]] (by Yang Shen. 20240113)
  * [[workshop:gamd | Reproduction of GaMD: Use GaMD to study combining of RNA and ligand ]] (by Yang Shen, 20251227)

====== NMR Assignment ======
  * [[workshop:nmr_assignment | NMR assignment]] (by Xu Ning, 20240404+20240511)

====== PDBLib ======
  * [[workshop:pdblib | PDBLib]] (by Prof. Xue, 20251025)
  * [[workshop:nass | Nass]] (by Prof. Xue, 20251206)

====== SHAPE ======
  * [[workshop:qushape | Use of QuShape]] (by Zhang Yikan, 20250614)
  * [[workshop:shape | RNA secondary structure mapping by SHAPE]] (by Zhang Yikan, 20240302)

====== Tools ======
  * [[workshop:aitools | Codes representation and sofware recommendation]] (by Zihang Zhou, 20240113)
  * [[workshop:copilot | Github Copilot]] (by Yuankuan Zhang, 20231202)

====== Older ones ======

===== Molecular Dynamics =====
[[ https://ambermd.org/Manuals.php | Manual Of Amber ]]

===== Machine Learning =====
Data cleaning (From Wang Banglong)

CS prediction (From Wang Banglong)

Data (From Qiu Haoren)

===== Cuda Programming =====
[[https://cloud.tsinghua.edu.cn/f/6e460d1035894f62b262 | CUDA by example (Chapter 1~5)]]

[[https://github.com/CodedK/CUDA-by-Example-source-code-for-the-book-s-examples- | and its source codes]]

===== NMR Textbook Chapters =====
Book-a: [[http://rainbow.life.tsinghua.edu.cn/~liun/Understanding_NMR_Spectroscopy-2rd_Edition.pdf | Understanding NMR Spectroscopy]] \\
Book-b: [[http://rainbow.life.tsinghua.edu.cn/~yxue/ebook/fundamentals_of_protein_nmr.pdf | Fundamentals of Protein NMR]] \\
Book-c: [[http://rainbow.life.tsinghua.edu.cn/~yxue/ebook/protein_nmr_spectroscopy.zip | Protein NMR Spectroscopy]]
  * <del>Book-a: 5.1-5.3 (Fourier transformation)</del>
  * <del>Book-a: 5.4-5.6 (Data processing)</del>
  * Book-a: chapter 13 (How the spectrometer works)
  * Book-a: chapter 6 (The quantum mechanics of one spin)
  * Book-a: chapter 7 (Product operators)
  * Book-a: 8.3-8.4 (COSY and DQF-COSY)
  * Book-a: 8.11; Book-b: 9.5; Book-c: 6.5 (TOCSY)
  * Book-b: Appendix D (Building Blocks of Pulse Sequences)
  * Book-b: 14.4 (Side-chain Assignment)

===== Pulse Sequence Analysis =====
  * Explain in details any pulse sequences that you think are interesting/useful

===== Paper Reading =====
  * [[http://rainbow.life.tsinghua.edu.cn/~xuelab/paper/ | Select 1-3 papers from any folder]]

====== Others ======
  * Any science-related stuff that you want to share with us
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