Dockstar 4 0

• pyDock - Protein-protein docking (see below for online) - standalone
• PrePPItar - Computational probing protein-protein interactions targeting small molecules - standalone
• DOVE - convolutional deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEtwork (DOVE) for evaluating protein docking models (online)
• EROS-DOCK - protein–protein docking using exhaustive branch-and-bound rotational search (standalone)
• INTERSPIA - Explore the Dynamics of Protein-Protein Interactions Among Multiple Species - online
• KSENIA - Knowledge of Native Protein-Protein Interfaces is Sufficient to Construct Predictive Models for the Selection of Binding Candidates (protein docking, knowledge-based potential) - standalone
• LightDock - a new multi-scale approach to protein-protein docking (standalone)
• MEPSA - Minimum energy pathway analysis for energy landscapes - standalone
• PRODIGY - Binding affinity of protein-protein complexes - standalone
• DOCKSCORE - A webserver for ranking protein-protein docked poses - online
• Galaxy - GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking - online
• HDOCK - hybrid protein–protein and protein–DNA/RNA docking (2017) - online
• DisVis - Visualizes the accessible interaction space - online
• DockStar - Modelling of multimolecular protein complexes - docking - online
• FiltRest3D - Filtering protein models by fuzzy restraints. Discrimination of native-like complexes from low-resolutions docking decoys - online and standalone
• InterEvDock - Docking server to predict the structure of protein–protein interactions using evolutionary information - online
• MinkoFit3D - A swebserver for fitting macromolecular assemblies into low-resolution electron density maps using Minkowski sum analysis - online
• (PS)2 - Prediction of protein complexes by comparative modeling(PS)2 - online
• pyDock - pyDockSAXS: Protein protein complex structure by SAXS and computational docking - online
• DockAFM - Docking structures under an AFM surface - online
• webSDA - A web server to simulate macromolecular diffusional association - online
• AIDA - Ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction - standalone and online server
• side chains - The Impact of Side-Chain Packing on Protein Docking Refinement - standalone
• Docks - AFM - Combine of docking solutions of structural subunits under an AFM surface (2014). CombineDocksAFM - online
• SPOT:RNA - SPOT-Seq-RNA: Predicting Protein-RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction - online
• LoopFinder - A web-based interface for LoopFinder (predict loops at interfaces, could be used for cmpd design) is currently under construction. In the meantime, LoopFinder is freely available for use. Requests for binary files or code can be sent to This email address is being protected from spambots. You need JavaScript enabled to view it. (Gavenonis et al, Nat Chem Biol. 2014) - standalone for now
• heparin - Heparin docking server for the identification of heparin binding sites on proteins (advanced option of the ClusPro server) - online
• PPI - Scoring docking conformations using predicted protein interfaces: T-PIP (For Protein Interface Prediction) and T-PioDock (For Ranking Docking Models) software - standalone
• DoBi - Find binding sites and can be used for docking - standalone
• Cell-Dock - High-performance protein-protein docking - standalone
• SEQMOL - Protein-protein docking: SEQMOL as a decoy filtering utility to select the best models - standalone
• Kd server - CRYSTAL STRUCTURE Kd SERVER (with SEQMOL). PDB to free energy (Alexei Korennykh lab). The algorithm was trained using experimentally determined binding parameters from about a hundred of different complexes. The software measures dG from calculating dS and dH of the interfaces. The paper will be published in the coming months - check with the authors
• Datasets - Complete Cross Docking Data Of Mintseris Benchmark 2.0 - dataset
• MFIB - Mutual Folding Induced by Binding (MFIB) database
• InterPreTS - Interaction Prediction through Tertiary Structure: Given a set of protein sequences (in fasta format), this tool will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction. Template-based docking - standalone
• Struct2Net - Struct2Net or Coev2Net Predict PPIs by combining a structure-based threading approach with machine learning techniques. Also compute a confidence score that addresses both false-positive and false-negative rates. Template-based docking - online
• Interact. - Interactome3D: a web service for the structural annotation of protein-protein interaction networks - online
• KBDOCK - KBDOCK (knowledge-based protein docking, docking under restraints) - database and online
• FunHunt - FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one) - online
• F2Dock - F2Dock, a rigid-body protein-protein docking software - online upon request
• BiGGER - Chemera is a molecular modelling and graphics application that also serves as the interface to BiGGER (protein-protein docking) - standalone
• FiberDock - Flexible Induced-fit Backbone Refinement in Molecular Docking. FiberDock is an efficient method for flexible refinement and re-scoring of rigid-body protein-protein docking solutions - online
• FRODOCK - Fast Rotational DOCKing. Generates very efficiently many potential predictions of how two proteins could interact - online
• DOCK - DOCK/PIE(RR): Web Server for Structure Prediction of Protein-Protein Complexes - online
• ZDOCK - ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers - online
• dDFIRE / DFIRE2 - Energy calculation - online
• PRISM - PRotein Interactions by Structural Matching - online
• DIMER - PREDDIMER: a web server for prediction of transmembrane helical dimers - online
• SPRING - SPRING is a template-base algorithm for protein-protein structure prediction - online
• COTH - COTH (CO-THreader) is a multiple-chain protein threading algorithm which is designed to identify and recombine protein complex structures from both tertiary and complex structure libraries - online
• TACOS - TACOS (Template-based Assembly of Complex Structures) is designed to model the structure of protein-protein complexes based on a hierarchical approach of template identification and structural refinement - online
• HOMCOS - HOmology Modeling of protein COmplex Structure - online
• Udock - The Interactive Docking Entertainment System - standalone (windows)
• DockTrina - Docking triangular protein trimers - docking, standalone
• DockRank - Ranking docked conformations using partner-specific sequence homology based protein interface prediction - online scoring
• MEGADOCK - An All-to-all Protein-protein Interaction Prediction System Using Tertiary Structure Data. Last version is 4, June 2014 - PPI docking, standalone
• Score-MI - An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking. The reduced alphabets derived from the present work were converted into a scoring function for the evaluation of docking solutions, which is available for public use via the web service score-MI - online scoring
• SymmDock - Prediction of Complexes with Cn Symmetry by Geometry Based Docking - online
• LZerD - Protein-Protein Docking Algorithm - standalone
• PI-LZerD - Protein Docking Prediction Using Predicted Protein-Protein Interface - standalone
• F(2)Dock 2.0 - Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank - PPI docking, online site 1
• F(2)Dock 2.0 - Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank - PPI docking, online site 2
• Link - PTools : a C++ and Python library for macromolecular docking - standalone
• ATTRACT - Docking Program (Fortran-Version, full source code and manual) - standalone
• SwarmDock - A server for flexible protein-protein docking - online docking
• Link - Prune and Probe: Two modular web services for protein-protein docking - docking online
• 3D-GARDEN - Global and Restrained Docking Exploration Nexus 3D-GARDEN is a state-of-the-art comprehensive software suite and server for protein-protein docking with full high-performance computing functionality - online docking
• Database - DOCKGROUND: The resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes - Database of experimental complexes
• FireDock - The server addresses the refinement problem of protein-protein docking solutions - Macromolecular docking online
• Grammx - Tools for protein-protein docking. GrammX: web interface of Gramm - Macromolecular docking online, see also standalone
• LIGIN - Molecular docking using surface complementarity. The LIGIN program is also available as part of WHATIF - standalone
• PatchDock - Protein docking tools (PatchDock) and related. PatchDock, webserver for macromolecules and small molecules docking based on shape complementarity criteria. There are many other tools here including tools for peptides, flexibility, comparing binding pockets.. - online docking
• AquaSAXS - A web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models - online
• PBSword - A web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database - online
• InterEvScore - A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution - standalone
• pyDockWEB - A web server that returns the best rigid-body docking orientations generated by FTDock and evaluated by pyDock scoring function, which includes electrostatics, desolvation energy and limited van der Waals contribution - online
• PyDock - Tool for protein-protein docking. The module ODA can help to predict potential protein-protein interaction regions. pyDock is a fast protocol which uses electrostatics and desolvation energy to score docking poses generated with FFT-based algorithms - standalone
• HINT - HINT (High-quality INTeractomes) is a database of high-quality protein-protein interactions in different organisms - database
• HADDOCK - Docking driven by interface restraints - online
• SmoothDock - Protein docking - docking online
• Bipdock - Bielefeld Protein Docking Software - standalone
• ZDOCK - docking based on FFT search - standalone
• ClusPro - Protein-protein docking webserver using 3 docking programs - DOT ZDOCK GRAMM - docking online
• PIC - Protein Interactions Calculator - online
• DOT - Protein-protein docking software - standalone
• ROSIE - ROSIE, including rosetta Protein-protein docking - online
• CombDock - Combinatorial assembly of multiprotein complexes by multiple docking (see also Firedock) - standalone
• RosettaDock - The RosettaDock server - docking
• BDOCK - Protein-protein docking software integrating the degree of burial of surface residues into protein-protein docking - standalone
• Hex - Protein-protein docking and molecular superposition program - docking online
• ESCHER-NG - Protein-protein and DNA-protein docking software - standalone
• FTDock - Fourier Transform Dock - standalone
• FastContact - : a free energy scoring tool for protein protein complex structures (PPI) - Scoring (PPI) online
• ADP_EM - Makes it possible to accurately dock atomic structures into low-resolution electron-density maps - standalone
• PARE - The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction - Structural Analysis, binding, mutations, online

• Dockstar 4 0 4
• Dockstar 4 0 2

• Last updated on .

DockStar is an add-on for the Apple Mail app which adds up to 5 new-mail indicators to the dock icon or to the System menu bar. Track email as it arrives in various accounts and local mailboxes. IMPORTANT Compatibility Note: DockStar is no longer supported in OS X 10.9 (Mavericks) or newer. Very fast layer 3/4 load balancing merged in Linux 2.4 and 2.6 kernels. Should be coupled with Keepalived to monitor servers. This generally is the solution embedded by default in most IP-based load balancers. Nginx ('engine X') Nginx is an excellent piece of software. DockStar offers a variety of T-track installation kits that provide everything needed to install a Smart Thruster onto your boat. Smart Thruster (Bow or Stern): $1,995. T-track Installation Kits: $125 - $350. This video shows how easy it is to retract the DockStar Smart Thruster by simply pulling in the lanyard. The Smart Thruster is deployed. 77 07 01 00 15 07 00 ff 01 01 62 1b 52 fe 55 00 00 00 00 01 - 21.7.0 (= Wirkleistung Bezug L1): 0 W 77 07 01 00 29 07 00 ff 01 01 62 1b 52 fe 55 00 00 00 00 01 - 41.7.0 (= Wirkleistung Bezug L2): 0 W 77 07 01 00 3d 07 00 ff 01 01 62 1b 52 fe 55 00 00 0a cf 01 - 61.7.0 (= Wirkleistung Bezug L3): 27.67 W. 自2005年，每年超过一亿的手机销售约98%至少使用了一个arm处理器 。 截至2009年，占大约90%的嵌入式32位risc处理器 和arm处理器被广泛使用在消费性电子产品，包括个人数字助理（pda）、平板电脑、移动电话、数字媒体和音乐播放器、手持式游戏游戏机、计算器和计算机外围设备（如硬盘.

From DP

• Bus Pirate v3.6 is also available at Adafruit Industries (USA) EpicTinker (USA) Watterott Electronic (Germany) Evola (Europe) Anibit (USA) Hackaday (USA)

The Bus Pirate is an open source hacker multi-tool that talks to electronic stuff. It's got a bunch of features an intrepid hacker might need to prototype their next project. This manual is an effort to link all available Bus Pirate information in one place.

• Read about the Bus Pirate v3 design; the v3b update; and the v3.5 update.

An initial batch of Bus Pirate v4 is now available to early adopters and testers. We think v3.x is still the best choice for most people, but v4 is the way of the future.

Introduction

Dockstar 4 0 4

Features

• Features overview (original)

Hardware

Tutorials

• Bus Pirate 101 tutorial (original)
• Bus Pirate 102 tutorial (original)

Forums

Linux, OS X

Download

kallisti5 has started a Bus Pirate community firmware project: to include the important fixes and clean-ups, committed by several prominent community members, and to continue its' future development.

Although the primary target of community is to significantly improve the user experience for Bus Pirate v4, the Bus Pirate v3 support will be maintained at all costs (despite the difficulties while compiling with the recent MPLAB XC16 compilers)

Source code and build instructions:

Latest builds of Bus Pirate community project (updated - 18th September 2016)

Contains:

• 1) BPv3 - different optimization firmware builds only (you could read why - at the bottom of this thread - https://github.com/BusPirate/Bus_Pirate/issues/7 )
• 2) BPv4 - three directories:

• 3) SHA1_checksums.txt inside each directory

About the optimization levels:

Even on level 3 my BPv4 passes a self test successfully, no errors. So you could try a stronger optimization first, and then - if it is causing you some issues - you tell us about them on Github and meanwhile could use a lighter optimization version (such as level 0 or 1)

Special builds of BPv3 firmware - extra features enabled!

Your feedback and patches are welcome! Here: Perchik wawe teil 4.

Old legacy stuff:

However, if for some reason you would like to install the official v6.1 firmware (almost 5 years old!), we wouldn't stop you. Here is a link to its' package:

Alternatively, you could get the sources for slightly newer (but still old) official v6.3 firmware:

but please note that you will need to compile it by yourself (cannot find a compiled hex file for it)

Reference

User terminal mode

The Bus Pirate is accessed from a command line in a serial terminal. The Bus Pirate always starts in high impedance mode (Hi-Z), a safe mode with all outputs disabled. It's intended to protect any connected devices from conditions beyond their specifications. From there, a bus mode can be selected to use the Bus Pirate with a specific protocol.

• Bus modes (main firmware): 1-Wire, UART, I2C, SPI, raw 2-wire, raw 3-wire, HD44780 LCDs, MIDI
• Bus modes (bonus firmware, v5.9+): PC keyboard, DIO, JTAG

Binary scripting mode

The Bus Pirate has a binary access mode that can be used with software or scripts. There's example scripts in C, Python, Perl, and more in the GitHub repository.

Binmode protocol pages: bitbang, SPI, I2C, UART, 1-Wire, and raw-wire.

A guide to getting started with the pyBusPirateLite Python library: Bus Pirate Scripting in Python

I/O header and hardware

Various probe cable pinouts

Application guides

Several applications can use the Bus Pirate as a programmer or debugger.

JTAG

The Bus Pirate is a slow serial port device intended for human-speed interaction. It was NEVER intended to do JTAG duties. Because it's open source, cheap, and versatile, the community hacked various JTAG features into it. They're great in a pinch, but no substitute for the real thing!

The Bus Pirate supports JTAG in three ways: with the OpenOCD debug application, as an XSVF player, and through a user-mode terminal interface.

JTAG and OpenOCD

The Bus Pirate is supported as a JTAG programmer/debugger by OpenOCD. If your target is supported by OpenOCD it may work. Slowly :) You will need to use a Bus Pirate firmware version which supports the binary JTAG protocol — not all do.

Note that the above is about binary JTAG / OpenOCD support. JTAG terminal mode is not enabled in any of the above firmwares (not even 5.9-extras, even though it was advertised to be enabled in there at some point).

FPGA and CPLD programming

As a stand-alone XSVF player to program CPLDs/FPGAs. This requires a simple firmware swap.

JTAG terminal mode

The -extras firmware has a the old user terminal JTAG mode from the Hack a Day demo. This was removed from the main firmware because nobody used it - it isn't particularly useful to enter JTAG commands manually. (OpenOCD uses the binary JTAG mode, which is different from the user terminal JTAG mode.)

AVR programming

The Bus Pirate can be used to program Atmel AVR microcontrollers. AVRDUDE version 5.8 and later support the Bus Pirate as a programmer directly. AVRDude is the most common software for programming AVR microcontrollers. Many packages such as WinAVR and the Arduino IDE bundle a version of AVRDude.

There is also an alternate firmware that can be installed on to Bus Pirate to make it an STK500 v2 AVR programmer clone.

• See Bus Pirate AVR Programming - Instructions and resources for AVR programming with the Bus Pirate.

flashrom

A flash chip programmer for Linux and Windows.

• flashrom bios/flash programmer (Latest Windows compile from forum)

Logic Analyzer with SUMP

The Bus Pirate can act as a low speed logic analyzer using a SUMP-compatible protocol. Jawi's latest OLS client includes extended support for the Bus Pirate.

• Logic analyzer mode (original)

Oscilloscope (very low speed)

• PirateScope in GIT (Python, Discussion)

Utilities

Chip demonstrations

Here's a comprehensive list of Bus Pirate chip demonstrations. It includes Ian's old demonstrations from Hack a Day, and the most recent demos from Dangerous Prototypes. Tutorials are arranged by Bus Pirate hardware version.

Bus Pirate v4

Bus Pirate v2&v3

• MMA7455L 3-axis accelerometer (SPI, IC2)
• 3EEPROM explorer board (original), DS2431 (1wire), 24AA (I2C), 25AA (SPI)
• Wii Nunchuck quick guide (original) (I2C)
• iButton serial number (original) (1-Wire)
• 2AA02E48 EEPROM with MAC address (original) (I2C)
• HD44780 LCD adapter v2 (LCD)
• DS1307 real time clock (original) (I2C)
• NA204SD02 Futaba VFD character display (raw2wire)
• SLE4442 (FedEx Kinko's) smart card update (original) (raw2wire)
• 25AA/25LC serial EEPROM (SPI)
• ShiftBrite with A6281 3 channel LED driver (SPI)
• PCF8563 real time clock calendar (I2C)
• Sure LED matrix (original) (raw3wire)
• AT45DB041D 4Mbit flash memory (original) (SPI)
• HMC6352 digital compass (original) (I2C)
• Parallax RFID reader (original) (UART)
• KS0074 serial LCD (original) (SPI)
• SURE DE-DP014 character matrix (raw3wire)
• 23K256 32K serial RAM (SPI)
• DS28EA00 temperature sensor (1-Wire)
• MCP9800 temperature sensor (I2C)
• DS18S20 temperature sensor (1-Wire) (Original)

Bus Pirate v1a

• LTC2640 digital to analog converter (SPI, raw3wire)
• LTC2631A digital to analog converter (I2C)
• PC keyboard (PC Keyboard)
• DS1807 audio volume potentiometer (I2C)
• SparkFun 4×4 RGB button pad controller (raw3wire)
• DS1801 audio volume potentiometer (SPI)
• MCP6S26 programmable gain amplifier (raw3wire)

Bus Pirate v0a

• 24LC1024 EEPROM (I2C)
• EM406 GPS (UART)
• SLE4442 (FedEx Kinko's) smart card (raw2 wire)
• DS1077 133MHz programmable oscillator (I2C)
• XC9572XL CPLD (JTAG)
• DS1822 temperature sensor (1-Wire)
• PCF8574 IO Expander (I2C)
• DS2431 1K EEPROM (1-Wire)
• SHT1x/7x humidity and temperature sensor (raw2wire)
• TC74 temperature sensor (I2C)

User submitted hacks and demos

• Wii Motion Plus controller (I2C)
• Nokia 3310 LCD (binary SPI)
• Hack the MD80 firmware to remove the date display (SPI sniffer)
• Program STM32 (raw2wire)
• I2C magnetic compass sensor (I2C)
• TK-1315LA GPS (serial UART)
• MAX147 ADC (SPI)
• MMA7456L three-axis accelerometer (I2C/SPI)
• FSA03 GPS (serial UART)
• Wavecom GSM modem (serial UART bridge)
• Zeno zit zapper tip reset (I2C)
• 1-Wire iButton (1-Wire)
• Bus Pirate high voltage power supply (PWM)
• Sniffing between smartcard & terminal (serial UART at arbitrary baudrate)
• AK8975 magnetometer (I2C)
• TMP102 temperature sensor (I2C)
• MMA8453Q accelerometer (I2C)
• Thinkpad T30 password reset (I2C)
• BPv4 HD66717 I2C demo (I2C)

Bus Pirate Education Kit

• mentioned in Workshop Video 52, and a preliminary DIP and nylon breadboard friendly parts manifest, pending a formal webpage with lab experiment write-ups

Firmware upgrades

Instructions for changing the firmware in a Bus Pirate over USB.

Updating Bus Pirate v4

Updating Bus Pirate v3

This section is for Bus Pirate v3.x with bootloader version 4+. See the next section for more bootloader information.

• Pirate-Loader console upgrade application (Linux, Mac, Windows) (original)
• ds30 Loader GUI (original) (Mono/.NET)

Follow these instructions to load new firmware, older firmware (v4+ only), the extras firmware, or the XSVF player firmware.

Bus Pirate v3 bootloader upgrades

The bootloader is a small program in the Bus Pirate that installs the firmware upgrade. Deadline 8 0 4 1 download free. The bootloader itself can also be upgraded with a small amount of effort. This is not normally required.

Program with a programmer

How to put the bootloader in a new chip or replace a damaged bootloader.

Hardware documentation

Bus Pirate v3.x

v3.6 is a minor update to v3 available from June 2012. All changes are cosmetic, v3.6 works exactly the same as previous v3s.

v3a, v3b, and v3.5 were available from October 2009 to June 2012. A similar version is sold by SparkFun.

• v3b hardware overview (original)
• v3a hardware overview (original)

v3.x is based on the original v2go circuit using a PIC24FJ64GA002 microcontroller.

Bus Pirate v4.x

v4 is currently in development. The first batch is available, but the hardware is still experimental.

• See it come to life, v4 development history and prototypes

Legacy hardware

Bus Pirate v2go was the first USB Bus Pirate. Around 1000 were sold as a fundraiser for Hack a Day. The PCB is black.

v1a and v0a were serial port Bus Pirate prototypes. Fundamental Logic briefly sold a through-hole kit for v1a.

Mods

Known Defects

Manufacturing resources

We maintain a combined bootloader/firmware flash image to assist in manufacturing.

• bpv3-BL44FW510-DUMP.hex is bootloader v4.4 with firmware v5.10

There is also an automated self-test utility, but it is generally slower than doing it manually Infographics maker 3 3 3 – templates bundle for pages.

Cases and accessories

• LCD adapter v2 ($9)
• Probe cable ($4.99)
• Synthetos laser-cut acrylic case ($14.99)
• Bus Pirate LCD adapter v1 deprecated

Source

License

Dockstar 4 0 2

• PCB art: CC-0
• Bootloader: GPL (from ds30 Loader project)
• Firmware: CC-0
• The Bus Pirate pinout, menu, and command tables are released into the public domain.