1. Folders

amber: forcefield: two force fields gaff: introduction of the General Amber Force Field (GAFF) implicit: recommendation from Carlos Simmerling for freezing local structure in simulation install: installation of amber16 (simplified since Amber20) optionand parameter: interpretation of options (to do) setup: usage of ParmEd and PROPKA tutorial: summary of tutorials tutorial01: tutorial for Accelerated MD (aMD) tutorial02: tutorial for MM-PBSA
cuda: introduction of CUDA config: configuration of CUDA and VSCode installation: installation of CUDA driver and the cuda toolkit
doku: something about Dokuwiki mathjax: the mathjax extension (parsing of TeX math expressions in wiki)
english: self-explained common: some common used expressions diffgood: a comment "Difference between Good, very Good, Excellent and Outstanding" exact: (???) jargon: collections of some specifically-used words or expressions
englishwriting: self-explained tense01: quotation from CSDN, about the tense in English writing tense02: another quotation from MuChong
ibiology: an online lesson baker: introduction to protein design by David Baker cheng: introduction to Cyro-EM by Yifan Cheng pyle: RNA by Anna Marie Pyle suess: Synthetic biology by Beatrix Suess
lab: something about the lab consumable: a list of consumables most in use (outdated) consumable_new: updated version at 2020 (outdated) duty: daily duties (not used any more) itemnew , items and reagents: location of the items
linux: usage of linux cookbook: tricks, such as how to change hostname troubleshooting: some troubles wsl: introduction of wsl (to do)
nmr: things about NMR 2d-plot: (???) assignment: self-explained, to be filled after the workshop by Xu Ning ebook: some textbooks experiment: STD and waterlogsy (outdated) paper: papers of Pulse sequence (link expired) protocol: self-explained pulseq_pzhou: (???) qa: some Q&As rate: rate of several universities rdc: alignment media and others request: collection of everyone's request (outdated) simulation: Recommend software, such as QSim, Spinach and others software: a brief comment of software used in NMR standard: (???) tutorial: ENC tutorials (expired)
office: Things about the Microsoft Office powerpoint: tricks about PPT word: tricks about word
playground: intended for practicing the DokuWiki syntax, replaced by sandbox now playground
protocol: some protocols rna_invitro, spcsh3, t7_extract, thermomixer, ubiquitin
pub: reserved for the lab's introduction and achievements members, publications, research, software
pymol: cookbook
python: cookbook
roadmap: (???) surui
sandbox: self-explained, used to get customed with DokuWiki, similar to the playground htmltest, orphan, zyk
scientist: adorable scientists -dcase
sudoku: more advanced techniques for sudoku advance
ubuntu: things about the operation system Ubuntu cookbook: some tricks gateway: notices of the net configuration latex: installation and setup of LaTex troubleshooting
wiki: things about the wiki dokuwiki: introduction of DokuWiki syntax: tutorial of the syntax welcome: one of the very first pages of one's DokuWiki
yxue: private space of Yi Xue lixinming, mi, music01, music_diamonds-and-rust, ra, tmp

2. Tutorials

aa is the summary of amino acids
bloch contains some GitHub repositories for block equation calculation
color brings a color chart with 140 colors' names, codes and RGBs
cpp provides two tutorials for learning C++
density introduce electron density map's concept and related softwares
english and englishwriting shows much useful knowledge
find_cds is a guidance for searching specific CDS region
GPU teaches us GPU programming
resources collects some common online tools
rnaocr is a tutorial about Optical Character Recognition (OCR)
sudoku provides a sudoku lesson
svd introduces Singular Value Decomposition (SVD) which is a math concept
sysbak teaches us how to backup the Ubuntu
wavelet interpret the difference between Fourier Transform (FT) and Wavelet Transform
docking provides several docking methods

3. Softwares

3.1. For research

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a molecular simulation program
CNS (Crystallography & NMR System) is used in macromolecular structure determination
ColabFold is used for protein structure prediction
CPPTRAJ is the main program in Amber for processing coordinate trajectories and data files
CS-Rosetta (Chemical-Shift-Rosetta) is a set of tools that allow efficient use of NMR chemical shifts to perform de novo protein structure determination
DSSP (Dictionary of Secondary Structure in Proteins) is an algorithm to standardize secondary structure assigment based on atomic coordinates
DSSR (Dissecting the Spatial Structure of RNA) is an integrated software tool for the analysis/annotation, model building, and schematic visualization of 3D nucleic acid structures
FOLDTRAJ is a program to generate plausible random protein structures
Gaussian 16 is the software for QM (quantum mechanics)
GROMACS is a versatile package to perform molecular dynamics, similar to CHARMM and AMBER.
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments
Modeller is a program for comparative protein structure modelling by satisfaction of spatial restraints
NMRPipe is a UNIX-based collection of programs and scripts for manipulating multidimensional NMR data
NMRViewJ is a Software for NMR visualization and analysis
PALES (Prediction of AlignmEnt from Structure) is a software for for analysis of residual dipolar couplings
Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography) is a comprehensive software package for macromolecular structure determination for crystallographic (X-ray, neutron, and electron) and electron cryo-microscopy data
Pymol is a software for 3D visualization and analysis of biological macromolecules
Rosetta software suite includes algorithms for computational modeling and analysis of protein structures
SHIFTS uses empirical formulas to estimate proton chemical shifts in proteins and nucleic acids
SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input
TopSpin is Bruker's standard NMR software used in a wide range of workflows
UFold is a deep learning-based method for RNA secondary structure prediction
VARNA is Java lightweight Applet dedicated to drawing the secondary structure of RNA
AutoDock Vina is an open-source program for doing molecular docking
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
VnmrJ is used for NMR Data processing and acquisition
X-PLOR is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH

3.2. For Linux usage

ambsync is a shell alias for duplicating md simulations with minimal necessary configurations
gpust is a shell alias for printing the occupation status for GPU cards on each server
apt-get is the software management software in Ubuntu
awk is a Linux program used to select particular records in a file and perform operations upon them
CentOS is one of the most popular Linux distributions
Copilot can provide contextualized assistance for programmers, from code completions to code explanations
Cygwin is a large collection of GNU and Open Source tools which provide functionality similar to a Linux distribution on Windows
Debian is one of the most popular Linux distributions
grep is a Linux program to search input files for matches of patterns
grub is a boot loader which is the first software program than runs when a computer starts
ImageMagick is a software suite used for editing and manipulating digital images
IPMI (Intelligent Platform Management Interface) is a protocol for remote computer management that enables operations independent of the system
Samba is the standard Windows interoperability suite of programs for Linux and Unix.
Slackware is one of the Linux distributions
tar is a Linux program to create tar files and extract tar archives
Thunderbird is a free all-platform email application
Ubuntu is one of the most popular Linux distributions
Vim is a highly configurable text editor
x2go is a software to enable you to access a graphical desktop of a computer over a low bandwidth (or high bandwidth) connection

3.3. For programming

bio3d is a package in R language
java is one of the programming languages
javascriptis one of the most popular programming languages
MariaDB Server is one of the world’s most popular open source relational databases
MATLAB is a programming and numeric computing platform used b to analyze data, develop algorithms, and create models
matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python
MySQL is a database server
perl is one of the programming language
PyGTK is a set of Python bindings to the popular GTK Toolkit
Python is one of the most popular programming languages
R is a programming language for data analysis and visualization
seaborn a Python data visualization library based on matplotlib

3.4. Others

Endnote is a software for reference management
LabVIEW (Laboratory Virtual Instrument Engineering Workbench) is a graphical programming environment that provides unique productivity accelerators for test system development
Lighttpd is a secure, fast, compliant, and very flexible web server
markdown is a simple and easy-to-use markup language you can use to format virtually any document
MathType is a famous equation editor, available as an Add-In for Work and PPT
Mendeley is a reference manager
onlinetool is a page for some online tools, such as pdf to png
phpMyAdmin is a free software tool written in PHP, intended to handle the administration of MySQL over the Web
Raspberry Pi is your tiny, powerful $35 computer
SCI-Hub is a website providing mass and public access to research papers
Windows contains some tricks about the Win operation system, from Yi Xue
YouTube is a set of online downloaders for YouTube videos.

4. Wet experiment

gencode illustrates the relationship between codons and corresponding amino acids
highpressurecraker: notes and troubleshooting
isotope
m9
nmr
order
protocol
recipe
rna_synthesis
sdsstaining

5. Server

6. Lab

7. Others

yxue

Table of Contents

1. Folders

2. Tutorials

3. Softwares

3.1. For research

3.2. For Linux usage

3.3. For programming

3.4. Others

4. Wet experiment

5. Server

6. Lab

7. Others