--- Log opened Thu Jul 21 00:00:03 2016 00:12 -!- augur [~augur@2601:645:c100:63f1:987b:8afe:55d:74ac] has joined ##hplusroadmap 00:38 < nmz787_i> .wik F. W. Aston  00:38 < yoleaux> nmz787_i: Sorry, that command (.wik) crashed. 00:38 < kanzure> since ribosome is a ribozyme, we can copy-paste most of the catalytic domains from ribozyme rna polymerase and turn that into a giant polymerase. 00:39 < kanzure> and synthetases have been fairly well engineered 00:39 < nmz787_i> .wik Francis William Aston 00:39 < yoleaux> "Francis William Aston FRS (1 September 1877 – 20 November 1945) was an English chemist and physicist who won the 1922 Nobel Prize in Chemistry for his discovery, by means of his mass spectrograph, of isotopes, in a large number of non-radioactive elements, and for his enunciation of the whole number rule. He was a fellow of the Royal …" — https://en.wikipedia.org/wiki/Francis_William_Aston 00:41 < kanzure> the same azobenzene amino acid can be reused in multiple places inside the same target protein, so optical illumination can cause multiple simultaneous changes 00:41 < nmz787_i> kanzure: you think catalysis of aminos and/or handling them will be so similar? 00:41 < kanzure> you would have to replace the catalytic domains 00:42 -!- ebowden [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has quit [Remote host closed the connection] 00:42 < nmz787_i> but holding aminos must be somewhat different too 00:42 -!- ebowden [~ebowden@2001:8003:100e:c500:7d1c:ed9a:a6e6:4a06] has joined ##hplusroadmap 00:42 < nmz787_i> so now you have to replace the binding domains too 00:42 < nmz787_i> what is left? 00:42 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-dcrpjzenrjdoqghj] has quit [Quit: Connection closed for inactivity] 00:44 < kanzure> synthetases. which are already well-studied well-engineered objects. 00:44 < nmz787_i> kanzure: is your comment because the azobenzene amino needs a non-standard ribosome ? 00:44 < nmz787_i> kanzure: synthetase is part of a ribosome? 00:45 < kanzure> synthetases bring amino acids to the ribosome 00:45 < kanzure> but they have been hacked to bring many other things 00:45 < nmz787_i> ah 00:45 < nmz787_i> hmm, that phenylazophenylalanine doesn't seem to be available on first-page google results 00:45 < kanzure> and they are much bigger than a single nucleotide, which is nice 00:48 < nmz787_i> hmm, so the azobenzene is basically the amino side-chain 00:48 < kanzure> yes the goal is to pick some residues to replace with that 00:49 < nmz787_i> well I guess I'd been incorrectly thinking it might have been mid-link 00:49 < nmz787_i> but that isn't how peptide chains are formed 00:50 < nmz787_i> mid-link meaning the chain would twist itself...with the sidechain it would need to twist and push on some other part of the molecule (peptide) 00:50 < nmz787_i> is there a python API to gromacs :) 00:51 < kanzure> nanoengineer had one 00:51 < nmz787_i> hmm, seems to be something 00:51 < kanzure> if not, it's trivial to write some bindings 00:54 < nmz787_i> if you swapped an amino in a PDB... making it 'too close' for room-temperature conditions... and put that into gromacs... might it reconfigure into a 'comfortable' energetic/molecular state? 00:57 < nmz787_i> hmm, I am looking for the inverse I think: http://bionano.physics.illinois.edu/nanoengineer2pdb 00:57 < nmz787_i> .title 00:57 < yoleaux> Converting NanoEngineer-1 DNA structure design (MMP file) to all-atom PDB file | The Aksimentiev Group 00:57 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 00:57 < nmz787_i> well, I see a lot of pdb files in the nanoengineer repo 00:57 < nmz787_i> so I guess they are supported by default 00:59 < nmz787_i> hmm, this seems to exist too? http://brlcad.org/coverage/brlcad/src/proc-db/pdb-g.c.gcov.html 01:00 < nmz787_i> .title https://web.archive.org/web/20020202141648/http://antas.agraria.uniss.it/software.html 01:08 -!- drewbot [~cinch@ec2-54-224-163-169.compute-1.amazonaws.com] has quit [Remote host closed the connection] 01:08 -!- drewbot [~cinch@ec2-23-23-53-202.compute-1.amazonaws.com] has joined ##hplusroadmap 01:18 < chris_99> https://adeshpande3.github.io/adeshpande3.github.io/A-Beginner%27s-Guide-To-Understanding-Convolutional-Neural-Networks/ 01:21 -!- maaku [~quassel@173-228-107-141.dsl.static.fusionbroadband.com] has quit [Ping timeout: 244 seconds] 01:23 -!- maaku [~quassel@173-228-107-141.dsl.static.fusionbroadband.com] has joined ##hplusroadmap 01:30 -!- ebowden [~ebowden@2001:8003:100e:c500:7d1c:ed9a:a6e6:4a06] has quit [Remote host closed the connection] 01:31 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: Malvolio] 01:40 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 276 seconds] 01:46 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 01:48 -!- ebowden [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has joined ##hplusroadmap 01:49 -!- ebowden [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has quit [Remote host closed the connection] 01:49 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has joined ##hplusroadmap 02:00 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 02:04 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 244 seconds] 02:15 -!- augur [~augur@2601:645:c100:63f1:987b:8afe:55d:74ac] has quit [Remote host closed the connection] 02:29 -!- Filosofem [~Jawmare@unaffiliated/jawmare] has joined ##hplusroadmap 02:32 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has quit [Ping timeout: 272 seconds] 03:16 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 03:37 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 258 seconds] 03:44 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 03:50 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 250 seconds] 04:26 -!- FourFire [~FourFire@51.175.137.57] has joined ##hplusroadmap 04:41 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 04:47 -!- bluebear_ [~chatzilla@80.95.97.194] has joined ##hplusroadmap 05:00 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 05:07 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 250 seconds] 05:18 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 260 seconds] 05:57 -!- eudoxia [~eudoxia@r167-57-138-88.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 06:00 -!- Aurelius_Work [~cpopell@209.48.69.2] has joined ##hplusroadmap 06:24 -!- Filosofem is now known as Jawmare 06:26 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-icpttcjiazksreml] has joined ##hplusroadmap 06:38 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 264 seconds] 06:41 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 06:52 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 07:04 < kanzure> erqierjaoifdjqoifjqoiqouiaofdajdioq 07:38 -!- eudoxia_ [~eudoxia@r167-57-5-99.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 07:42 -!- eudoxia [~eudoxia@r167-57-138-88.dialup.adsl.anteldata.net.uy] has quit [Ping timeout: 252 seconds] 07:48 -!- c0rw1n [~c0rw1n@116.47-244-81.adsl-dyn.isp.belgacom.be] has quit [Ping timeout: 240 seconds] 08:06 -!- eudoxia_ [~eudoxia@r167-57-5-99.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 08:13 -!- JayDugger [~jwdugger@108.19.186.58] has joined ##hplusroadmap 08:16 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Quit: Leaving] 08:17 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 08:27 -!- Gurkenglas [Gurkenglas@dslb-178-005-223-183.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 08:55 < ybit_> https://theconversation.com/all-you-need-for-quantum-computing-at-room-temperature-is-some-mothballs-62549 08:55 < ybit_> http://www.nature.com/ncomms/2016/160718/ncomms12232/full/ncomms12232.html 09:06 -!- FourFire [~FourFire@51.175.137.57] has quit [Quit: Leaving] 09:16 < kanzure> .title http://www.nature.com/ncomms/2016/160718/ncomms12232/full/ncomms12232.html 09:16 < yoleaux> Room temperature manipulation of long lifetime spins in metallic-like carbon nanospheres : Nature Communications : Nature Research 09:21 < kanzure> anselm complaining about dna storage ideas https://news.ycombinator.com/item?id=8999919 09:22 < kanzure> "If we get a little scifi, and assume we build programmable polymerases and get nanopore (direct read) sequencing. Even then, physics limits you to something like 1000 read/writes per sec per pore/polymerase. Instrumenting to these will probably limit per-feature size to being larger than 100micron on a fabricated chip, giving us an ultimate read/write limit around: (2cm/100um)^2 x 1000 bit/sec = 40Mbit/sec for a giant 2cmx2cm chip. With ... 09:22 < kanzure> ... the necessary error-correction and redundancy, it's probably going to cap out around 1Mbit/sec at best. Those 700TB take about 2months to read/write at these rates, and we'll have much-better solid state storage technologies by the time we figure out how to all that with DNA." 09:22 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-icpttcjiazksreml] has quit [Quit: Connection closed for inactivity] 09:26 < kanzure> here's a bunch of polymerases, nucleotidyl transferases, primases, and poly(A) polymerases in the form of pdb files http://diyhpl.us/~bryan/papers2/polymerase/polymerases.pdb.tar.xz (41 MB) 09:27 -!- ArturSha1 [~ArturShai@37.218.162.107] has quit [Ping timeout: 272 seconds] 09:46 < kanzure> dna polymerase mu and TdT seem to be functionally similar 09:49 < kanzure> "Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region" http://nar.oxfordjournals.org/content/early/2009/06/05/nar.gkp460.short 09:49 < kanzure> "... a deletion of the entire Loop1 as in pol λ does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol μ Loop1 reproduces pol μ behavior" 09:54 -!- rhaps0dy_ [~rhaps0dy@81.4.122.176] has joined ##hplusroadmap 10:09 -!- Gurkenglas [Gurkenglas@dslb-178-005-223-183.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 244 seconds] 10:22 < kanzure> "standard tailing protocols" 10:39 -!- c0rw1n [~c0rw1n@2a02:2788:936:490:323a:64ff:fee6:8994] has joined ##hplusroadmap 10:44 -!- Burninate [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has quit [Ping timeout: 240 seconds] 10:47 -!- bluebear_ [~chatzilla@80.95.97.194] has quit [Quit: ChatZilla 0.9.92 [Firefox 47.0/20160606113944]] 10:56 -!- Burninate [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has joined ##hplusroadmap 10:58 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 11:02 -!- Regex_ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Ping timeout: 250 seconds] 11:03 -!- SloanOnLinux [~sloan@162.72.132.128] has joined ##hplusroadmap 11:08 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 11:15 < CaptHindsight> http://www.glenresearch.com/ProductFiles/Product.php?item=10-5800 Azobenzene Phosphoramidite 11:16 < CaptHindsight> 0.25g $550.00 11:20 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has quit [Remote host closed the connection] 11:23 < kanzure> yep 11:23 < kanzure> it's useful 11:24 < kanzure> but also, i'm really excited about those azobenzene amino acids. v. useful for protein conformational changes. 11:25 -!- nildicit [~nildicit@unaffiliated/nildicit] has quit [Ping timeout: 244 seconds] 11:30 < CaptHindsight> http://www.glenresearch.com/Catalog/catalog.php?page=droligo#p18 price drop 11:31 < CaptHindsight> when I looked a few months ago there was a slew of cappers, decappers , linkers etc 11:31 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-xopsegmecxvsekgf] has quit [Quit: Connection closed for inactivity] 11:32 < CaptHindsight> you just need to decide how you are going to build your synthesizer 11:32 < CaptHindsight> and find someone to build it for you 11:33 < kanzure> don't forget the ligation part. it's just dna hybridization array stuff without ligation and conjugation. 11:33 < kanzure> *stuff if you go without ligation and conjugation. 11:35 < CaptHindsight> it's all out there 11:35 < kanzure> here is a good chapter on "Catalytic mechanism of DNA polymerases" from 2010, http://www.bc.sinica.edu.tw/MDTsai/2010/CNPII%20349-383.pdf 11:35 < CaptHindsight> take your pick 11:36 < kanzure> page 372 (page 25) has a section on molecular dynamics simulations 11:36 < kanzure> CaptHindsight: hm? 11:37 < CaptHindsight> I keep telling you but you you made some comment about "hand waving" which I assumed to be projection 11:37 < kanzure> CaptHindsight: there's no good option yet for dna ligation on an inkjet bed, i proposed one method using reservoire flow (which it turns out that twist biosciences is also using at the moment), and EWOD, and micropipetting (which does not scale well for large amounts of DNA) 11:37 < kanzure> and EWOD might require oil-water emulsion techniques 11:38 < CaptHindsight> who cares if twist biosciences is using it? 11:39 < CaptHindsight> it's not likely for the FDA to approve anything open source 11:39 < kanzure> validation is super important 11:39 < CaptHindsight> from whom? 11:39 < kanzure> if someone tried for years and spent zillions, and it didn't work, then you should avoid it. if they have validated the method, then that's a good signal. 11:40 < CaptHindsight> or they hired idiots 11:40 < CaptHindsight> most often what I discover 11:41 < CaptHindsight> but there's plenty of working chemistry out there 11:46 -!- Regex_ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 11:50 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Ping timeout: 250 seconds] 11:50 < chris_99> CaptHindsight, i just found myself a robot arm http://www.ebay.co.uk/itm/Sintron-Mini-Industrial-Robotic-Arm-Kit-DIY-Robot-Toy-Servos-Joystick-UNO-R3-/151832587078 ;) 11:51 < chris_99> could be a fun toy for my desk 11:53 -!- nildicit [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 11:53 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has joined ##hplusroadmap 11:54 < CaptHindsight> hobby servos 11:55 < CaptHindsight> not closed loop but fun 11:55 < chris_99> ah, do hobby servos not have an encoder on? 11:56 < chris_99> i thought servo means, there is always a feedback loop 11:57 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has joined ##hplusroadmap 11:58 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has quit [Ping timeout: 260 seconds] 12:03 < CaptHindsight> https://www.princeton.edu/~mae412/TEXT/NTRAK2002/292-302.pdf 12:04 < CaptHindsight> the feedback is just inside the motor 12:04 < CaptHindsight> the controller just outputs PWM 12:17 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:21 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has quit [Ping timeout: 244 seconds] 12:29 -!- Aurelius_Work [~cpopell@209.48.69.2] has quit [Ping timeout: 250 seconds] 12:31 -!- Aurelius_Work [~cpopell@209.48.69.2] has joined ##hplusroadmap 12:35 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Ping timeout: 240 seconds] 12:35 -!- sandeepkr_ [~sandeep@111.235.64.4] has joined ##hplusroadmap 12:38 < chris_99> oh interesting 12:47 -!- sandeepkr__ [~sandeep@111.235.64.4] has joined ##hplusroadmap 12:50 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Read error: No route to host] 12:51 -!- sandeepkr_ [~sandeep@111.235.64.4] has joined ##hplusroadmap 12:51 < CaptHindsight> chris_99: if you really want to play here's a $25K arm for ~$1k http://www.ebay.com/itm/Staubli-RX60-Robot-Arm-With-Base-/201628876886 12:52 < chris_99> now that looks more like it 12:53 < chris_99> i'm in the UK alas, i've seen some for like £400 before 12:53 < chris_99> though 12:53 < CaptHindsight> ^^ they have ~10um repeatability 12:53 < CaptHindsight> so goof for tissue engineering 12:53 < chris_99> 10um?!!!! 12:53 < CaptHindsight> goof/good 12:53 < chris_99> thats amazing 12:54 -!- Aurelius_Work2 [~cpopell@209.48.69.2] has joined ##hplusroadmap 12:54 < CaptHindsight> http://www.staubli.com/en/robotics/6-axis-scara-industrial-robot/low-payload-6-axis-scara-robot/6-axis-industrial-robot-tx60/ 12:55 -!- sandeepkr__ [~sandeep@111.235.64.4] has quit [Ping timeout: 250 seconds] 12:55 < CaptHindsight> they spec them at 20um at full load and at top speed, but they can hold much better 12:56 -!- Aurelius_Work [~cpopell@209.48.69.2] has quit [Ping timeout: 244 seconds] 13:10 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has joined ##hplusroadmap 13:25 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has quit [Ping timeout: 276 seconds] 13:33 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has joined ##hplusroadmap 13:36 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Ping timeout: 240 seconds] 13:38 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has quit [Ping timeout: 260 seconds] 13:44 -!- SloanKloan [~sloan@162.72.132.128] has joined ##hplusroadmap 13:47 -!- SloanOnLinux [~sloan@162.72.132.128] has quit [Ping timeout: 240 seconds] 14:02 -!- jaboja [~jaboja@2a00:f41:383e:4b61:de85:deff:fe55:967a] has joined ##hplusroadmap 14:05 < kanzure> how is it that there are aptamers that bind in picomolar concentration, how does that work.. 14:10 < kanzure> hrm i should ping genehacker at some point 14:12 < btcdrak> probably off topic but http://www.theverge.com/2016/7/21/12247370/police-fingerprint-3D-printing-unlock-phone-murder 14:16 -!- jaboja [~jaboja@2a00:f41:383e:4b61:de85:deff:fe55:967a] has quit [Ping timeout: 264 seconds] 14:16 -!- nmz787_i [~ntmccork@134.134.139.76] has quit [Quit: Leaving.] 14:20 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has joined ##hplusroadmap 14:23 -!- jaboja [~jaboja@2a00:f41:383e:4b61:de85:deff:fe55:967a] has joined ##hplusroadmap 14:30 -!- nmz787_i [ntmccork@nat/intel/x-lssjyuiaipndtuse] has joined ##hplusroadmap 14:31 -!- nmz787_i [ntmccork@nat/intel/x-lssjyuiaipndtuse] has left ##hplusroadmap [] 14:34 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has joined ##hplusroadmap 14:36 < kanzure> parahsailin points out that azobenzene switching time might be too slow for our purposes 14:37 -!- Aurelius_Work2 [~cpopell@209.48.69.2] has quit [Ping timeout: 244 seconds] 14:39 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has quit [Ping timeout: 260 seconds] 14:42 < kanzure> we need a good rational protein design conspiracy theory or two... if this was working, do you think anyone would really want to tell everyone that "hey protein design works"? 14:53 -!- SloanKloan [~sloan@162.72.132.128] has left ##hplusroadmap ["Once you know what it is you want to be true, instinct is a very useful device for enabling you to know that it is"] 14:53 -!- SloanOnLinux [~sloan@162.72.132.128] has joined ##hplusroadmap 15:00 < kanzure> re: restriction of protein engineering to only those spiral shapes or whatever. i think that needs to be double checked. i think some of the protein folding is solved for. so we should find some good chases in existing proteins. then paste catalytic protein domains to that, run selection experiments and get improved proteins with known-simulatable backbones and folding. and next most of biology should be replaced with only those ... 15:00 < kanzure> ... structures, since it's more convenient for us to work with. 15:24 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has quit [Ping timeout: 272 seconds] 15:25 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has joined ##hplusroadmap 15:28 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has joined ##hplusroadmap 15:33 -!- ebowden [~ebowden@2001:8003:100e:c500:9170:7d7a:27be:3b7a] has quit [Ping timeout: 260 seconds] 15:34 -!- ebowden [~ebowden@2001:8003:100e:c500:b920:4764:a438:7c04] has joined ##hplusroadmap 15:37 -!- c0rw1n [~c0rw1n@2a02:2788:936:490:323a:64ff:fee6:8994] has quit [Ping timeout: 264 seconds] 15:37 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 15:41 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 252 seconds] 15:41 -!- esmerelda [~mabel@unaffiliated/jacco] has joined ##hplusroadmap 15:43 < kanzure> i think foldit is assuming that all protein folding predictions can be solved by trying to predict and score the lowest minimum energy configuration or something 15:43 < kanzure> so they are assuming that all proteins fold in this way 15:51 -!- andyphoneshi [~androirc@172.56.7.208] has joined ##hplusroadmap 15:57 -!- andyphoneshi [~androirc@172.56.7.208] has left ##hplusroadmap ["AndroIRC"] 15:58 -!- andyphoneshi [~androirc@172.56.7.208] has joined ##hplusroadmap 16:01 -!- c0rw1n [~c0rw1n@116.47-244-81.adsl-dyn.isp.belgacom.be] has joined ##hplusroadmap 16:02 -!- jaboja [~jaboja@2a00:f41:383e:4b61:de85:deff:fe55:967a] has quit [Ping timeout: 264 seconds] 16:05 -!- ebowden [~ebowden@2001:8003:100e:c500:b920:4764:a438:7c04] has quit [Remote host closed the connection] 16:06 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 16:07 -!- ebowden [~ebowden@2001:8003:100e:c500:7509:63ac:f59c:96e3] has joined ##hplusroadmap 16:07 < kanzure> http://foldit.wikia.com/wiki/Research_Chat_Room 16:12 < kanzure> .wik intrinsically unstructured proteins 16:12 < yoleaux> "An intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure. IDPs cover a spectrum of states from fully unstructured to partially structured and include random coils, (pre-)molten globules, and large multi-domain proteins connected by flexible linkers." — https://en.wikipedia.org/wiki/Intrinsically_unstructured_proteins 16:13 -!- mmnnnnnggg [~androirc@2605:6000:fb44:9900:4daf:b8df:636:88a8] has joined ##hplusroadmap 16:15 < kanzure> slide 8 is pretty interesting (simulation vs experiment for protein folding) http://web.stanford.edu/class/cs279/lectures/lecture5.pdf 16:16 -!- ebowden [~ebowden@2001:8003:100e:c500:7509:63ac:f59c:96e3] has quit [Remote host closed the connection] 16:17 < kanzure> "Even sequences with 15% sequence identity usually have similar structures. • Also, there only appear to be 1,000–10,000 naturally occurring protein folds." 16:18 < andyphoneshi> kanzure 1000-10000 types (and many per protein) or only that many protein shapes total? 16:20 < kanzure> http://www.sbg.bio.ic.ac.uk/phyre2/html/flibview.cgi?pdb=c5b42A_ 16:20 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 240 seconds] 16:20 < kanzure> andyphoneshi: not sure 16:21 < andyphoneshi> Heh, the latter would be awesome, the former is pretty forboding 16:21 < kanzure> i am a little skeptical about the "just find the most energy minimizing shape" goal... there doesn't seem to be any study showing this is a good assumption. 16:21 < andyphoneshi> ..this in general is a good physical assumption, you can derive tons of chemistry from it 16:22 < kanzure> fold.it has a heuristic scoring function for energy minimization, so it appears to me that they should just try to randomly generate answers and then score them. what's the big deal? it's not even running molecular dynamics. 16:22 < andyphoneshi> mm ok that'll miss local minima ofc 16:22 < kanzure> it's "find the closest local minima and fall down the energy slope"? 16:23 < andyphoneshi> I would expect that 16:23 < andyphoneshi> based on the parts of science I have any familiarity with (not biochem :p) 16:26 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 276 seconds] 16:26 < kanzure> "Uses a large database of 3-residue and 9-residue fragments, taken from structures in the PDB" 16:26 < kanzure> (rosetta) 16:27 < maaku> what local analysis misses is that as the protien folds in on itself, the energy minima change 16:27 < kanzure> ouch.. so basically they are doing find-and-replace for chunks of residues at a time, then updating their free energy minimizing calculations for the rest of the residues in the protein to determine if that (found) shape wokrs. 16:27 < maaku> with naturally occuring genes at least there's a lot of non-intuitive folds because of this effect 16:27 < maaku> easy to engineer around that with designed proteins though 16:28 < kanzure> yeah i am still interested in finding a subset of proteins and amino acid residues that we can say are simpler to simulate and fold 16:28 < kanzure> if the spiral or helical proteins are easier, then fine, let's slap on some catalytic domains and then optimize them through some rounds of selection, and replace all of biology with those proteins instead of whatever nasty folds we're currently using 16:29 < maaku> kanzure: I suspect the key point will be designing DNA origami like interconnects between active sites 16:29 < maaku> right ok what you just said :) 16:31 < kanzure> it is not clear to me if there's a subset of amino acids that are easier to fold and calculate energy for.. 16:31 < andyphoneshi> Presumably the ones we have are in some strong sense the simplest .. since we hit them by chance first 16:32 < kanzure> well one guess would be something like "find amino acids that are mostly inert" 16:42 < kanzure> "How do small single-domain proteins fold?" http://www.sciencedirect.com/science/article/pii/S1359027898000339 16:42 < maaku> andyphoneshi: or easier to create by natural process, which means more existing by default 16:43 < maaku> probably lots of astrobiology research relevant to this question 16:48 -!- harold [~poetry@li354-248.members.linode.com] has quit [Remote host closed the connection] 17:04 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has quit [Ping timeout: 276 seconds] 17:14 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 17:24 < kanzure> hm even the alpha helix stuff seems to have weird folding properties 17:34 -!- esmerelda [~mabel@unaffiliated/jacco] has quit [Ping timeout: 264 seconds] 17:36 -!- streety [streety@2a01:7e00::f03c:91ff:feae:ded6] has quit [Quit: ZNC - http://znc.in] 17:36 -!- ebowden [~ebowden@1.136.97.109] has joined ##hplusroadmap 17:43 -!- mmnnnnnggg [~androirc@2605:6000:fb44:9900:4daf:b8df:636:88a8] has quit [Ping timeout: 250 seconds] 17:44 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has joined ##hplusroadmap 17:48 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 17:49 -!- streety [~streety@jonathanstreet.com] has joined ##hplusroadmap 17:49 -!- ebowden [~ebowden@1.136.97.109] has quit [Ping timeout: 260 seconds] 17:54 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 250 seconds] 18:00 < kanzure> "Rational design of α-helical tandem repeat proteins with closed architectures" http://www.nature.com/nature/journal/v528/n7583/abs/nature16191.html 18:15 < kanzure> "Exploring the repeat protein universe through computational protein design" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845728/ 18:21 < kanzure> "linear repeat protein" 18:28 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:31 -!- psyreal [~psyreal@c-67-189-81-15.hsd1.wa.comcast.net] has quit [Read error: Connection reset by peer] 18:46 -!- ebowden [~ebowden@147.69.145.152] has joined ##hplusroadmap 18:50 < CaptHindsight> kanzure: I've been watching genetic engineering since the early 80's but just recently decided to get involved since it's taking so damn long. 18:52 < CaptHindsight> so far I don't see any conspiracy other than publicized connections between presidents, congress and drug co's, I mostly see idiots with accountants that manage to show millions spent on R&D that could cost a few % of what they say they spend 18:52 < kanzure> no no, i mean protein design not genetic engineering 18:53 < kanzure> protein design is commonly said to be hard due to protein folding-- but often that's handwaving because discussion of the actual problems don't occur afterwards. 18:53 < kanzure> using a constrained set of amino acids and other techniques, like highly repetitive sequences of amino acids, you can predict with high accuracy the shape of the resulting protein 18:55 < kanzure> while that's still "hard to simulate" at an atomistic level, you don't have to simulate it at all because you already know the result ahead of simulation time 18:56 < kanzure> http://diyhpl.us/~bryan/papers2/bio/protein-engineering/ 18:58 < CaptHindsight> an extension of polymer chemistry 19:04 < CaptHindsight> with an emphasis on folding 20:01 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 20:09 -!- ArturSha1 [~ArturShai@37.218.162.107] has joined ##hplusroadmap 20:39 < nmz787> welp, basically a no-go on SERS single-nucleotide 20:39 < nmz787> glad I was inspired to get into crazy high-performance analog though 20:48 -!- ebowden [~ebowden@147.69.145.152] has quit [Remote host closed the connection] 20:51 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-btywdxuhimyxlrro] has joined ##hplusroadmap 20:53 -!- ebowden [~ebowden@1.136.96.129] has joined ##hplusroadmap 21:03 -!- ebowden [~ebowden@1.136.96.129] has quit [Remote host closed the connection] 21:12 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Ping timeout: 240 seconds] 21:28 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 21:38 -!- ebowden [~ebowden@1.136.96.203] has joined ##hplusroadmap 21:45 < kanzure> why's that? 21:48 < nmz787> doesn't perform as hoped/proposed 21:48 < nmz787> noise 22:01 -!- ebowden [~ebowden@1.136.96.203] has quit [Remote host closed the connection] 22:03 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 22:08 -!- saturn2 [~visitant@unaffiliated/clone-of-saturn/x-2509460] has quit [Ping timeout: 276 seconds] 22:25 -!- Malvolio is now known as Guest28852 22:25 -!- Guest28852 [~Malvolio@unaffiliated/malvolio] has quit [Killed (tepper.freenode.net (Nickname regained by services))] 22:25 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 22:34 -!- ebowden [~ebowden@1.136.97.105] has joined ##hplusroadmap 22:44 -!- saturn2 [~visitant@unaffiliated/clone-of-saturn/x-2509460] has joined ##hplusroadmap 22:49 -!- ebowden [~ebowden@1.136.97.105] has quit [Ping timeout: 260 seconds] 22:51 -!- ebowden [~ebowden@147.69.145.152] has joined ##hplusroadmap 22:58 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:07 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:07 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 23:07 -!- Burnin8 [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has joined ##hplusroadmap 23:10 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 250 seconds] 23:10 -!- Regex_ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Ping timeout: 250 seconds] 23:10 -!- Burninate [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has quit [Ping timeout: 250 seconds] 23:14 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Read error: Connection reset by peer] 23:14 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:18 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Read error: Connection reset by peer] 23:19 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:20 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Read error: Connection reset by peer] 23:20 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:21 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Read error: Connection reset by peer] 23:22 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:22 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Read error: Connection reset by peer] 23:23 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 23:28 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 276 seconds] 23:29 -!- andyphoneshi [~androirc@172.56.7.208] has quit [Ping timeout: 240 seconds] 23:30 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has joined ##hplusroadmap 23:35 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 23:42 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has quit [Read error: Connection reset by peer] 23:43 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has joined ##hplusroadmap 23:45 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has quit [Client Quit] --- Log closed Fri Jul 22 00:00:03 2016