[{"data":1,"prerenderedAt":281},["ShallowReactive",2],{"project-41448439":3},{"id":4,"name":5,"line":6,"line_source":7,"title":8,"url":9,"domain":10,"maker":11,"posted_at":12,"year":13,"points":14,"comments":15,"rank_in_year":16,"shown_in_year":17,"top":18,"tier":19,"category":20,"subcategory":21,"format":22,"keywords":23,"reception":28,"sentiment":29,"stance_mix":30,"scored_comments":35,"aspects":36,"strip":41,"post_text":43,"what":44,"said":75,"maker_in_thread":129,"shape":136,"grid":141,"attempts":242,"same_week":243,"maker_shows":34,"maker_hidden":273,"reader_version":274,"card":275},"41448439","AlphaFold3","An open-source implementation of AlphaFold3","title","Show HN: An open-source implementation of AlphaFold3","https:\u002F\u002Fgithub.com\u002FLigo-Biosciences\u002FAlphaFold3","github.com","EdHarris",1725471857,2024,314,37,188,3515,6,"legend","ai","protein structure prediction","library",[21,24,25,26,27],"alphafold3","open source","pytorch","drug discovery","curious",0.071,{"positive":31,"neutral":32,"mixed":33,"critical":34},3,9,0,1,13,{"docs":37,"performance":38,"execution":39,"idea":40},{"positive":33,"critical":33},{"positive":33,"critical":33},{"positive":33,"critical":33},{"positive":33,"critical":33},[31,33,31,33,31,33,42,33,34,33,33,33,33,33,33,33,33,33,33,33,33,33,33,42,31,33,33,33,31,31,33,42,31,33,31,31,33],5,"Hi HN - we’re the founders of Ligo Biosciences and are excited to share an open-source implementation of AlphaFold3, the frontier model for protein structure prediction.\n\nGoogle DeepMind and their new startup Isomorphic Labs, are expanding into drug discovery. They developed AlphaFold3 as their model to accelerate drug discovery and create demand from big pharma. They already signed Novartis and Eli Lilly for $3 billion - Google’s becoming a pharma company! (https:\u002F\u002Fwww.isomorphiclabs.com\u002Farticles\u002Fisomorphic-labs-kicks-off-2024-with-two-pharmaceutical-collaborations)\n\nAlphaFold3 is a biomolecu",{"problem":45,"audience":51,"pricing":59,"motivation":60,"time_to_build":59,"stack":67,"openness":72,"stage":73,"team_size":74},{"value":46,"source":47,"evidence":48},"AlphaFold3 code and weights were not released, so researchers could not use it under a commercial-friendly license","maker",[49],{"id":50},"post",{"value":52,"source":47,"evidence":53},"Biotech and pharma companies and researchers needing protein structure prediction",[54,55],{"id":50},{"id":56,"by":57,"text":58},"41451243","boldlybold","Thanks for releasing this, I've been looking forward to a truly open version I can use in a commercial setting. What a way to launch the company!",null,{"value":61,"source":47,"evidence":62},"Build enzyme design tools for chemical manufacturing and open source a fundamental model for the community",[63,66],{"id":64,"by":11,"text":65},"41449070","Our long term goal is to design enzymes for chemical manufacturing. We decided to build AlphaFold3 because we had seen how useful AlphaFold2 had been for the protein design…",{"id":50},[68],{"value":69,"source":47,"evidence":70},"PyTorch",[71],{"id":50},"open_source","beta","company",{"praise":76,"objections":82,"requests":97,"questions":102,"alternatives":117},[77],{"value":78,"source":79,"evidence":80},"Welcomed as a truly open version usable commercially","commenter",[81],{"id":56,"by":57,"text":58},[83,90],{"value":84,"source":79,"evidence":85},"Name may infringe DeepMind's trademark; implementation is not truly AlphaFold3",[86],{"id":87,"by":88,"text":89},"41449933","dekhn","You probably want to change the name of this implementation as it's not truly AlphaFold3. I wouldn't be surprised if you got a C&D from DM for using the name.",{"value":91,"source":79,"evidence":92},"Weights and benchmarks not yet released; model only partially trained",[93,96],{"id":94,"by":11,"text":95},"41451063","The predictions can be verified by comparing the predicted structure to the experimentally solved structure, either crystal or cryoEM. The model is still training and improving,…",{"id":50},[98],{"value":99,"source":79,"evidence":100},"Rename the project",[101],{"id":87,"by":88,"text":89},[103,110],{"value":104,"source":79,"evidence":105},"What is the business plan and what is being sold",[106],{"id":107,"by":108,"text":109},"41448989","lacker","This seems really neat! DeepMind and AlphaFold are clearly moving in a closed-source direction, since they created Isomorphic Labs as a division of Alphabet essentially focused…",{"value":111,"source":79,"evidence":112},"How are predictions verified against experiment",[113],{"id":114,"by":115,"text":116},"41450570","dwayne_dibley","Hi, how are predictions verified? Does one still do experimental techniques (X-ray crystallography, cryogenic-em etc.) one you have the prediction? Or are predictions so close to…",[118,122],{"value":119,"source":47,"evidence":120},"OpenFold",[121],{"id":50},{"value":123,"source":79,"evidence":124},"ColabFold",[125],{"id":126,"by":127,"text":128},"41453870","inciampati","Are you familiar with ColabFold? https:\u002F\u002Fgithub.com\u002Fsokrypton\u002FColabFold",{"comments":32,"answered":18,"key":130},[131,132,135],{"id":64,"text":65},{"id":133,"text":134},"41449491","OpenFold, which was AlphaFold2's open-source implementation was published in Nature Methods. We will prepare a similar publication once the model is more mature and when we have…",{"id":94,"text":95},{"commenters":137,"max_depth":138,"maker_replies":32,"first_comment_mins":139,"lifespan_hours":140},21,7,35,43,[142,144,146,150,151,154,155,157,160,163,165,169,173,176,178,181,183,185,188,191,193,195,198,200,202,206,208,211,213,218,221,224,226,229,231,235,238],[107,33,31,143,108,33],"maker\u002Fneutral\u002Fnone",[64,33,33,145,11,34],"maker\u002Fneutral\u002Fidea",[147,34,31,148,149,33],"41449322","maker\u002Fneutral\u002Fdocs","fngjdflmdflg",[133,34,33,148,11,34],[114,152,31,153,115,33],2,"maker\u002Fneutral\u002Fperformance",[94,152,33,153,11,34],[56,31,42,156,57,33],"project\u002Fpositive\u002Fnone",[158,31,33,159,11,34],"41451491","maker\u002Fpositive\u002Fnone",[87,161,34,162,88,33],4,"project\u002Fcritical\u002Fnone",[164,161,33,143,11,34],"41450006",[166,42,33,167,168,33],"41449014","other\u002Fneutral\u002Fnone","snolbert",[170,42,33,171,172,33],"41449387","commenter\u002Fneutral\u002Fnone","nolist_policy",[174,42,33,171,175,33],"41449684","lofatdairy",[177,42,33,171,88,33],"41451095",[179,42,33,171,180,33],"41452183","natechols",[182,42,33,171,88,33],"41452226",[184,42,33,171,175,33],"41460935",[186,42,33,171,187,33],"41452047","throwaway48476",[189,18,33,167,190,33],"41450513","benreesman",[192,18,33,171,11,34],"41450760",[194,18,33,167,190,33],"41451321",[196,18,33,171,197,33],"41452757","MylesHollowed",[199,18,33,171,190,33],"41452982",[201,18,42,159,190,33],"41453094",[203,138,31,204,205,33],"41457339","project\u002Fneutral\u002Fperformance","westurner",[207,138,33,204,11,34],"41458849",[209,138,33,171,210,33],"41465719","flobosg",[212,138,33,171,210,33],"41465775",[214,215,31,216,217,33],"41454999",8,"project\u002Fneutral\u002Fexecution","londons_explore",[219,215,31,216,220,33],"41455223","littlestymaar",[222,215,33,223,11,34],"41458828","maker\u002Fneutral\u002Fexecution",[225,215,42,159,220,33],"41465645",[227,32,31,145,228,33],"41448948","ck_one",[230,32,33,145,11,34],"41449117",[232,32,31,233,234,33],"41452265","project\u002Fneutral\u002Fidea","ricopags",[126,236,31,237,127,33],10,"project\u002Fneutral\u002Fnone",[239,240,33,167,241,33],"41448800",11,"serial_dev",[],[244,249,254,258,263,268],{"id":245,"name":246,"points":247,"category":248},"41416714","Linkpreview",362,"dev_tools",{"id":250,"name":251,"points":252,"category":253},"41444855","tetris-sql",338,"games",{"id":255,"name":256,"points":257,"category":253},"41424371","Defrag the Game",326,{"id":259,"name":260,"points":261,"category":262},"41389176","solar concentrator",296,"hardware",{"id":264,"name":265,"points":266,"category":267},"41424954","Broadcast Box",283,"infrastructure",{"id":269,"name":270,"points":271,"category":272},"41436338","Repaint",236,"web_saas",false,"v2",{"id":276,"name":5,"line":6,"ai":273,"cat":20,"year":13,"points":14,"comments":15,"rec":28,"s":277,"top":18,"kw":278,"maker":11,"domain":10,"tier":19,"attempts":33,"strip":279,"url":9,"mix":280,"praise":78,"objection":84,"sub":21},41448439,0.07,[21,24,25,26,27],"3030305010000000000000053000330530330",[31,32,33,34],1794036660473]