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Table of Contents
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)
- lab: something about the lab consumable: a list of consumables most in use (outdated) consumable_new: updated version at 2020 (outdated) duty: daily duties (not used any more) itemnew , items and reagents: location of the items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self-explained, to be filled after the workshop by Xu Ning ebook: some textbooks experiment: STD and waterlogsy (outdated) paper: papers of Pulse sequence (link expired) protocol: self-explained pulseq_pzhou: (???)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some Q&As rate: rate of several universities rdc: alignment media and others request: collection of everyone's request (outdated) simulation: Recommend software, such as QSim, Spinach and others software: a brief comment of software used in NMR standard: (???)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
- pymol: cookbook
- python: cookbook
- roadmap: (???) surui
- 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
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)
- 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
5. Server
6. Lab
7. Others
navigation.txt · Last modified: 2024/04/03 12:18 by 127.0.0.1
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