Dockstar 4 0

adminApril 27 2021

Dockstar 4 0

The best on the water just got even better. MasterCraft’s new DockStar Handling System gives drivers of any ability a boost of confidence by making tight spots like docks and marinas easier to navigate. DockStar’s breakthrough design delivers the ultimate control with a system of additional rudders that deflect prop wash beneath the boat. Oct 08, 2010 Seagate's FreeAgent DockStar Network Adapter is the successor to its FreeAgent GoDock+, the optional docking station for Seagate's line of Seagate FreeAgent Go portable drives.DockStar sets the Go. HTC Desire, SBM7000, Oregon State University OSWALD, Gumstix Overo Earth, Pandora, Apple iPhone 3GS, Apple iPod touch (3rd and 4th Generation), Apple iPad, Apple iPhone 4, Apple TV (Second Generation), Archos 5, Archos 43, BeagleBoard, Genesi EFIKA MX, Motorola Droid, Motorola Droid X, Motorola Droid 2, Motorola Droid R2D2 Edition, Palm Pre. 3.1-4.1 litres/ha in 200 litres of water/ha or spot application. Use the high rate on heavy infestations of mature docks. Dockstar may cause temporary yellowing of some pasture species. To minimise any check to growth do NOT spray immediately after grazing. Leave pasture for at least 2-3 weeks after grazing before spraying.

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

Last updated on .

Audio

alsa-utils should supply the needed programs to use onboard sound. Defaultvolume can be adjusted using alsamixer.

A key change with Linux kernel version 4.4.x for ARM related to ALSA and to theneeded sound module: in order to use tools such as alsamixer with the currentkernel, users must modify /boot/config.txt to contain the following line:

Caveats for Audio

To force audio over HDMI, add this to /boot/config.txt:

If you experience distortion using the 3.5mm analogue output:

Bluetooth

firmware

To be able to talk to the bluetooth chip, you must install the services, firmware, and UDEV rules. The pi-bluetooth packagefrom the AUR is available to do this.

wifi-coexistence

The BCM43* series chips are notorious for problems when both wifi and bluetooth are used at the same time. This coexistence issue comes in varying degrees of severity but for most users makes using the Pi in bluetooth A2DP mode while also using wifi impossible. Bluetooth buffer underruns are caused by sharing the UART device, resulting in skipping, popping, hissing, and generally unusable audio. For some users, this also effects peripherals such as mice and keyboards. A firmware fix was found for both the Pi3 and Pi ZeroW, discussion of this fix can be found in this github issue.

To deploy the fix to the current firmware in Arch add the following lines:

to the end of these firmware config files:

/usr/lib/firmware/updates/brcm/brcmfmac43430-sdio.txt

/usr/lib/firmware/updates/brcm/brcmfmac43455-sdio.txt

This fix can be found in this git commit. The fix is experimental and is not yet deployed to the upstream package

Video

4 Divided By 0 Equals

The X.org driver for Raspberry Pi can be installed with the xf86-video-fbdev or xf86-video-fbturbo-git package.

CPU/GPU RAM split

Memory split between the CPU and GPU can be set in boot/config.txtby adjusting the parameter gpu_mem which stands for the amount of RAM in MBthat is available to the GPU (minimum 16, default 64) and the rest is availableto the ARM CPU.

HDMI/Analogue TV-Out

With the default configuration, the Raspberry Pi uses HDMI video if a HDMImonitor is connected. Otherwise, it uses analog TV-Out (also known as compositeoutput or RCA) To turn the HDMI or analog TV-Out on or off, have a look at/opt/vc/bin/tvservice

Use the -s parameter to check the status; the -oparameter to turn the display off and -p parameter to power on HDMI withpreferred settings.

Adjustments are likely required to correct properoverscan/underscan and are easily achieved in /boot/config.txt in which manytweaks are set. To fix, simply uncomment the corresponding lines and setup perthe commented instructions:

Or simply disable overscan if the TV/monitor has a 'fit to screen' option.

Users wishing to use the analog video out should consult this config filewhich contains options for non-NTSC outputs.

Camera

The commands for the camera module are included as part of the raspberrypi-firmware package:$ /opt/vc/bin/raspistill$ /opt/vc/bin/raspivid

Append to /boot/config.txt:gpu_mem=128start_file=start_x.elffixup_file=fixup_x.datOptionally

The following is a common error:

which can be corrected by setting these values in /boot/config.txt:cma_lwm=cma_hwm=cma_offline_start=

Another common error:mmal: mmal_vc_component_create: failed to create component 'vc.ril.camera' (1:ENOMEM)mmal: mmal_component_create_core: could not create component 'vc.ril.camera' (1)mmal: Failed to create camera componentmmal: main: Failed to create camera componentmmal: Only 64M of gpu_mem is configured. Try running 'sudo raspi-config' and ensure that 'memory_split' has a value of 128 or greater

can be corrected by adding the following line to /etc/modprobe.d/blacklist.conf:

In order to use standard applications (those that look for /dev/video0) theV4L2 driver must be loaded. This can be done automatically at boot by creatingan autoload file, /etc/modules-load.d/rpi-camera.conf:

The V4L2 driver by default only allows video recording up to 1280x720, else itglues together consecutive still screens resulting in videos of 4 fps or lower.Adding the following options removes this limitation, /etc/modprobe.d/rpi-camera.conf:

Onboard Hardware Sensors

Dockstar 4 000

Temperature

Temperatures sensors can be queried with utils in the raspberrypi-firmware package.

Voltage

Four different voltages can be monitored via /opt/vc/bin/vcgencmd:

Where <id> is:

core for core voltage
sdram_c for sdram Core voltage
sdram_i for sdram I/O voltage
sdram_p for sdram PHY voltage

Watchdog

BCM2708 has a hardware watchdog which can be utilized by enabling thebcm2708_wdog kernel module.

For proper operation the watchdog daemon also has to be installed, configured(by uncommenting the 'watchdog-device' line in /etc/watchdog.conf) andenabled.

This should also apply for Raspberry Pi 2 by using the bcm2709_wdog moduleand Raspberry Pi 3 by using the bcm2835_wdt module.

Hardware Random Number Generator

Arch Linux ARM for the Raspberry Pi had the bcm2708-rng module set to load atboot; starting with kernel 4.4.7 the bcm2835_rng module replaces theformer on Raspberry Pi 2 and Raspberry Pi 3 units.

Install rng-tools andtell the Hardware RNG Entropy Gatherer Daemon (rngd) where to find the hardwarerandom number generator. This can be done by editing /etc/conf.d/rngd:

and enabling and starting the rngd service.

If haveged is running, it should be stopped and disabled, as it mightcompete with rngd and is only preferred when there is no hardware random numbergenerator available.

Once completed, this change ensures that data from thehardware random number generator is fed into the kernel's entropy pool at/dev/random. To check the available entropy, run:

The number it reports should be around 3000, whereas before setting up rngd itwould have been closer to 1000.

I/O Pins

GPIO

To be able to use the GPIO pins from Python, use the RPi.GPIO library. Install the python-raspberry-gpio packagefrom the AUR.

SPI

To enable the /dev/spidev* devices, uncomment the following line in/boot/config.txt:

I2C

Install i2c-tools and lm_sensors packages.

Configure the bootloader to enable the i2c hardware by appending to /boot/config.txt:

Configure the i2c-dev and i2c-bcm2708 (if not blacklisted for the camera) modules to be loaded at boot in/etc/modules-load.d/raspberrypi.conf:

i2c-dev i2c-bcm2708

Reboot the Raspberry Pi and issue the following command to get the hardware address:

Note: When using the I2C1 port instead of I2C0, one will need to run i2cdetect-y 1 instead and replace i2c-0 with i2c-1 in the following steps.

Now instantiate the device. Change the hardware address to the address found inthe previous step with '0x' as prefix (e.g. 0x48) and choose a device name:

Check dmesg for a new entry:

Finally, read the sensor output: sensors

1-WIRE

To enable the 1-wire interface add this line to /boot/config.txt and reboot.dtoverlay=w1-gpio

Non-Root GPIO

To use the GPIO/SPI pins as a regular non-root user (in group tty), add the following lines to a new file /usr/lib/udev/rules.d/99-spi-permissions.rules