# 1. Folders - amber: [forcefield](amber:forcefield): two force fields [gaff](amber:gaff): introduction of the General Amber Force Field (GAFF) [implicit](amber:implicit): recommendation from Carlos Simmerling for freezing local structure in simulation [install](amber:install): installation of amber16 (simplified since Amber20) [option](amber:option)and [parameter](amber:parameter): interpretation of options (to do) [setup](amber:setup): usage of ParmEd and PROPKA [tutorial](amber:tutorial): summary of tutorials [tutorial01](amber:tutorial01): tutorial for Accelerated MD (aMD) [tutorial02](amber:tutorial02): tutorial for MM-PBSA - cuda: introduction of CUDA [config](cuda:config): configuration of CUDA and VSCode [installation](cuda:installation): installation of CUDA driver and the cuda toolkit - doku: something about Dokuwiki [mathjax](doku:mathjax): the mathjax extension (parsing of TeX math expressions in wiki) - english: self-explained [common](english:common): some common used expressions [diffgood](english:diffgood): a comment "Difference between Good, very Good, Excellent and Outstanding" [exact](english:exact): (???) [jargon](english:jargon): collections of some specifically-used words or expressions - englishwriting: self-explained [tense01](englishwriting:tense01): quotation from CSDN, about the tense in English writing [tense02](englishwriting:tense02): another quotation from MuChong - ibiology: an online lesson [baker](ibiology:baker): introduction to protein design by David Baker [cheng](ibiology:cheng): introduction to Cyro-EM by Yifan Cheng [pyle](ibiology:pyle): RNA by Anna Marie Pyle [suess](ibiology:suess): Synthetic biology by Beatrix Suess - lab: something about the lab [consumable](lab:consumable): a list of consumables most in use (outdated) [consumable_new](lab:consumable_new): updated version at 2020 (outdated) [duty](lab:duty): daily duties (not used any more) [itemnew](lab:itemnew) , [items](lab:items) and [reagents](lab:reagents): location of the items - linux: usage of linux [cookbook](linux:cookbook): tricks, such as how to change hostname [troubleshooting](linux:troubleshooting): some troubles [wsl](linux:wsl): introduction of wsl (to do) - nmr: things about NMR [2d-plot](nmr:2d-plot): (???) [assignment](nmr:assignment): self-explained, to be filled after the workshop by Xu Ning [ebook](nmr:ebook): some textbooks [experiment](nmr:experiment): STD and waterlogsy (outdated) [paper](nmr:paper): papers of Pulse sequence (link expired) [protocol](nmr:protocol): self-explained [pulseq_pzhou](nmr:pulseq_pzhou): (???) [qa](nmr:qa): some Q&As [rate](nmr:rate): rate of several universities [rdc](nmr:rdc): alignment media and others [request](nmr:request): collection of everyone's request (outdated) [simulation](nmr:simulation): Recommend software, such as QSim, Spinach and others [software](nmr:software): a brief comment of software used in NMR [standard](nmr:standard): (???) [tutorial](nmr:tutorial): ENC tutorials (expired) - office: Things about the Microsoft Office [powerpoint](office:powerpoint): tricks about PPT [word](office:word): tricks about word - playground: intended for practicing the DokuWiki syntax, replaced by sandbox now [playground](playground:playground) - protocol: some protocols [rna_invitro](protocol:rna_invitro), [spcsh3](protocol:spcsh3), [t7_extract](protocol:t7_extract), [thermomixer](protocol:thermomixer), [ubiquitin](protocol:ubiquitin) - pub: reserved for the lab's introduction and achievements [members](pub:members), [publications](pub:publications), [research](pub:research), [software](pub:software) - pymol: [cookbook](pymol:cookbook) - python: [cookbook](python:cookbook) - roadmap: (???) [surui](roadmap:surui) - sandbox: self-explained, used to get customed with DokuWiki, similar to the playground [htmltest](sandbox:htmltest), [orphan](sandbox:orphan), [zyk](sandbox:zyk) - scientist: adorable scientists -[dcase](scientist:dcase) - sudoku: more advanced techniques for sudoku [advance](sudoku:advance) - ubuntu: things about the operation system Ubuntu [cookbook](ubuntu:cookbook): some tricks [gateway](ubuntu:gateway): notices of the net configuration [latex](ubuntu:latex): installation and setup of LaTex [troubleshooting](ubuntu:troubleshooting) - wiki: things about the wiki [dokuwiki](wiki:dokuwiki): introduction of DokuWiki [syntax](wiki:syntax): tutorial of the syntax [welcome](wiki:welcome): one of the very first pages of one's DokuWiki - yxue: private space of Yi Xue [lixinming](yxue:lixinming), [mi](yxue:mi), [music01](yxue:music01), [music_diamonds-and-rust](yxue:music_diamonds-and-rust), [ra](yxue:ra), [tmp](yxue:tmp) # 2. Tutorials - [aa](aa) is the summary of amino acids - [bloch](bloch) contains some GitHub repositories for block equation calculation - [color](color) brings a color chart with 140 colors' names, codes and RGBs - [cpp](cpp) provides two tutorials for learning C++ - [density](density) introduce electron density map's concept and related softwares - [english](english) and [englishwriting](englishwriting) shows much useful knowledge - [find_cds](find_cds) is a guidance for searching specific CDS region - [GPU](gpu) teaches us GPU programming - [resources](resources) collects some common online tools - [rnaocr](rnaocr) is a tutorial about Optical Character Recognition (OCR) - [sudoku](sudoku) provides a sudoku lesson - [svd](svd) introduces Singular Value Decomposition (SVD) which is a math concept - [sysbak](sysbak) teaches us how to backup the Ubuntu - [wavelet](wavelet) interpret the difference between Fourier Transform (FT) and Wavelet Transform - [docking](docking) provides several docking methods # 3. Softwares ## 3.1. For research - [CHARMM (Chemistry at HARvard Macromolecular Mechanics)](charmm) is a molecular simulation program - [CNS (Crystallography & NMR System)](cns) is used in macromolecular structure determination - [ColabFold](colabfold) is used for protein structure prediction - [CPPTRAJ](cpptraj) is the main program in Amber for processing coordinate trajectories and data files - [CS-Rosetta (Chemical-Shift-Rosetta)](csrosetta) 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)](dssp) is an algorithm to standardize secondary structure assigment based on atomic coordinates - [DSSR (Dissecting the Spatial Structure of RNA)](3dna) is an integrated software tool for the analysis/annotation, model building, and schematic visualization of 3D nucleic acid structures - [FOLDTRAJ](foldtraj) is a program to generate plausible random protein structures - [Gaussian 16](gaussian) is the software for QM (quantum mechanics) - [GROMACS ](gromacs) is a versatile package to perform molecular dynamics, similar to [CHARMM](charmm) and [AMBER](amber). - [HMMER](hmmer) is used for searching sequence databases for sequence homologs, and for making sequence alignments - [Modeller](modeller) is a program for comparative protein structure modelling by satisfaction of spatial restraints - [NMRPipe](nmrpipe) is a UNIX-based collection of programs and scripts for manipulating multidimensional NMR data - [NMRViewJ](nvj) is a Software for NMR visualization and analysis - [PALES (Prediction of AlignmEnt from Structure)](pales) is a software for for analysis of residual dipolar couplings - [Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography)](phenix) is a comprehensive software package for macromolecular structure determination for crystallographic (X-ray, neutron, and electron) and electron cryo-microscopy data - [Pymol](pymol) is a software for 3D visualization and analysis of biological macromolecules - [Rosetta](rosetta) software suite includes algorithms for computational modeling and analysis of protein structures - [SHIFTS](shifts) uses empirical formulas to estimate proton chemical shifts in proteins and nucleic acids - [SHIFTX2](shiftx2) predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input - [TopSpin](topspin) is Bruker's standard NMR software used in a wide range of workflows - [UFold](ufold) is a deep learning-based method for RNA secondary structure prediction - [VARNA](varna) is Java lightweight Applet dedicated to drawing the secondary structure of RNA - [AutoDock Vina](vina) is an open-source program for doing molecular docking - [VMD](vmd) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting - [VnmrJ](vnmrj) is used for NMR Data processing and acquisition - [X-PLOR](xplor) 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](ambsync) is a shell alias for duplicating md simulations with minimal necessary configurations - [gpust](gpust) is a shell alias for printing the occupation status for GPU cards on each server - [apt-get](apt-get) is the software management software in Ubuntu - [awk](awk) is a Linux program used to select particular records in a file and perform operations upon them - [CentOS](centos) is one of the most popular Linux distributions - [Copilot](copilot) can provide contextualized assistance for programmers, from code completions to code explanations - [Cygwin](cygwin) is a large collection of GNU and Open Source tools which provide functionality similar to a Linux distribution on Windows - [Debian](debian) is one of the most popular Linux distributions - [grep](grep) is a Linux program to search input files for matches of patterns - [grub](grub) is a boot loader which is the first software program than runs when a computer starts - [ImageMagick](imagemagick) is a software suite used for editing and manipulating digital images - [IPMI (Intelligent Platform Management Interface)](ipmi) is a protocol for remote computer management that enables operations independent of the system - [Samba](samba) is the standard Windows interoperability suite of programs for Linux and Unix. - [Slackware](slackware) is one of the Linux distributions - [tar](tar) is a Linux program to create tar files and extract tar archives - [Thunderbird](thunderbird) is a free all-platform email application - [Ubuntu](ubuntu) is one of the most popular Linux distributions - [Vim](vim) is a highly configurable text editor - [x2go](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](bio3d) is a package in R language - [java](java) is one of the programming languages - [javascript](javascript)is one of the most popular programming languages - [MariaDB Server](mariadb) is one of the world’s most popular open source relational databases - [MATLAB](matlab) is a programming and numeric computing platform used b to analyze data, develop algorithms, and create models - [matplotlib](matplotlib) is a comprehensive library for creating static, animated, and interactive visualizations in Python - [MySQL](mysql) is a database server - [perl](perl) is one of the programming language - [PyGTK](pygtk) is a set of Python bindings to the popular GTK Toolkit - [Python](python) is one of the most popular programming languages - [R](r) is a programming language for data analysis and visualization - [seaborn](seaborn) a Python data visualization library based on matplotlib ## 3.4. Others - [Endnote](endnote) is a software for reference management - [LabVIEW (Laboratory Virtual Instrument Engineering Workbench)](labview)  is a graphical programming environment that provides unique productivity accelerators for test system development - [Lighttpd](lighttpd) is a secure, fast, compliant, and very flexible web server - [markdown](markdown) is a simple and easy-to-use markup language you can use to format virtually any document - [MathType](mathtype) is a famous equation editor, available as an Add-In for Work and PPT - [Mendeley](mendeley) is a reference manager - [onlinetool](onlinetool) is a page for some online tools, such as pdf to png - [phpMyAdmin](phpmyadmin) is a free software tool written in PHP, intended to handle the administration of MySQL over the Web - [Raspberry Pi](raspberrypi) is your tiny, powerful $35 computer - [SCI-Hub](scihub) is a website providing mass and public access to research papers - [Windows](windows) contains some tricks about the Win operation system, from Yi Xue - [YouTube](youtube) is a set of online downloaders for YouTube videos. # 4. Wet experiment - [gencode](gencode) illustrates the relationship between codons and corresponding amino acids - [highpressurecraker](highpressurecraker): notes and troubleshooting - [isotope](isotope) - [m9](m9) - [nmr](nmr) - [order](order) - [protocol](protocol) - [recipe](recipe) - [rna_synthesis](rna_synthesis) - [sdsstaining](sdsstaining) # 5. Server - [IP](ipaddress) - [Configurations](server_info) - [ID of users](userid) # 6. Lab - [follow](follow) - [labfollow](labfollow) - [workshop](workshop) - [groupmeeting](groupmeeting) # 7. Others - [yxue](yxue)