tag:blogger.com,1999:blog-68318993169781980312024-03-17T20:03:54.296-07:00SIRAH ForcefieldSirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.comBlogger82125tag:blogger.com,1999:blog-6831899316978198031.post-33411721581228747182023-11-03T07:01:00.003-07:002023-11-03T08:17:36.498-07:00New Tutorials on Github!<p> <img alt="UBC GitHub Instructor Guide | Learning Technology Hub" aria-hidden="false" class="sFlh5c pT0Scc iPVvYb" jsaction="VQAsE" jsname="kn3ccd" src="https://lthub.ubc.ca/files/2021/06/GitHub-Logo.png" style="height: 263px; margin: 0px; max-width: 3840px; width: 467px;" /></p><p>Hi! we are migrating this page to Github. You can check out our new and restyled tutorials <a href="https://sirahff.github.io/documentation/index.html" target="_blank">here</a>. </p><p>They include new tips, warnings, and new tutorials for running and analyzing CG trajectories with SIRAHTools. </p><p>Special thanks to Andrés Ballesteros, Lucianna Silva, and Martín Soñora for their hard work!</p>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-4216513835215506182023-02-28T10:50:00.004-08:002023-02-28T10:51:24.746-08:00Back soon ...<p style="text-align: center;"> <img alt="WIP - Work In Progress or Waste In Progress ?" class="n3VNCb pT0Scc KAlRDb" data-noaft="1" jsaction="load:XAeZkd;" jsname="HiaYvf" src="https://media.licdn.com/dms/image/C5112AQFJSqouBrY4ig/article-cover_image-shrink_720_1280/0/1572274275044?e=2147483647&v=beta&t=ao-zM67PVdOOGtL_H9Auvk3mv9vAujah0HJ4NhzANrI" style="height: 345px; margin: 0px; width: 371.3541666666667px;" /></p><p style="text-align: center;">Dear SIRAH users, we have been out for a while. We are updating the force field and this page.</p><p style="text-align: center;">Meanwhile, you can download the current SIRAH version and related contents, as usual.</p>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-12005791147005222732020-05-09T07:28:00.000-07:002020-05-09T07:28:22.583-07:00New CG trajectories of SARS-CoV2 available<div style="text-align: center;">
<img alt="sirahcluster" height="320" src="https://www.cluster.uy/images/bannersirahclust.png" width="320" /></div>
<div style="text-align: center;">
<span style="font-size: large;">All CG simulations of SARS-CoV2 proteins and complexes are accessible from the web page of <a href="https://www.cluster.uy/web-covid/" target="_blank">ClusterUy</a> So far the following PDB structures have been simulated for 10 or more microseconds: </span></div>
<div style="text-align: center;">
<span style="font-size: large;"><a href="https://www.cluster.uy/web-covid/#6LU7">6LU7, </a><a href="https://www.cluster.uy/web-covid/#6YVO">6YVO, </a><a href="https://www.cluster.uy/web-covid/#6W01">6W01, </a><a href="https://www.cluster.uy/web-covid/#6M3M">6M3M, </a><a href="https://www.cluster.uy/web-covid/#6W4B">6W4B, </a><a href="https://www.cluster.uy/web-covid/#6W02">6W02, </a><a href="https://www.cluster.uy/web-covid/#6W9C">6W9C, </a><a href="https://www.cluster.uy/web-covid/#6W4H">6W4H, </a><a href="https://www.cluster.uy/web-covid/#6W41">6W41, </a><a href="https://www.cluster.uy/web-covid/#6YHU">6YHU.</a> </span></div>
<div style="text-align: center;">
<span style="font-size: large;">If you are interested in any particular system, just let us know.</span></div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com8tag:blogger.com,1999:blog-6831899316978198031.post-1066034561115043342020-05-05T14:28:00.001-07:002020-05-05T14:28:35.218-07:00We are within Amber2020!<div style="text-align: center;">
<img height="320px" src="https://ambermd.org/images/Amber20_cover.png" style="text-align: right;" vertical-align="center" width="260px" /></div>
<div style="text-align: center;">
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif; font-size: x-large;"><span style="color: black;">The SIRAH </span>ff 2.0<span style="color: black;"> forms part of the new </span>official <span style="color: black;">release of the </span><a href="https://ambermd.org/AmberTools.php" target="_blank">Amber20 package</a>.</span></div>
<div style="text-align: center;">
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif; font-size: x-large;"><br /></span></div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com1tag:blogger.com,1999:blog-6831899316978198031.post-5878227413877328232020-04-15T11:08:00.002-07:002020-04-15T11:11:37.165-07:00The SIRAH-CoV2 initiative: new trajectories available (PDB ids: 6LU7, 6W02)<span style="background-color: rgba(255 , 255 , 255 , 0.7); font-family: "cambria"; font-size: 16px;"><br /></span>
<br />
<span style="font-size: large;">The trajectories and topologies of the main protease (15 microseconds, PDBid: 6LU7) and ADP ribose phosphatase of NSP3 from SARS-CoV2 (10 microseconds, PDBid: 6W02) provided as raw data in Amber format have just been uploaded to the <a href="https://zenodo.org/search?page=1&size=20&q=SIRAH-CoV2&keywords=SIRAH">Zenodo Database</a>. </span>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com2tag:blogger.com,1999:blog-6831899316978198031.post-14248619722214732972020-04-12T06:51:00.001-07:002020-04-12T10:34:43.079-07:00The SIRAH-CoV2 initiative: freely available coarse-grained simulations of SARS-CoV2 proteins<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-KKgUPjn5jGfbPK-uvMICyIelauDfOiHPP6MibCvtIxQUo7TlgEpjnT5os-C3XoHAhNkZefpkdVbldAyG4OQmP6ZFMPJrboIuL8KjyTJiRq_BEVVKBRNY0FumAxIe7mFSBGv2EDNPNOvq/s1600/6lu7.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="198" data-original-width="219" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-KKgUPjn5jGfbPK-uvMICyIelauDfOiHPP6MibCvtIxQUo7TlgEpjnT5os-C3XoHAhNkZefpkdVbldAyG4OQmP6ZFMPJrboIuL8KjyTJiRq_BEVVKBRNY0FumAxIe7mFSBGv2EDNPNOvq/s1600/6lu7.gif" /></a></div>
<span lang="EN-US" style="font-family: "cambria"; font-size: 12pt;">The Group of Biomolecular Simulations at the Institut Pasteur de Montevideo, and the National Supercomputing Center (Cluster-UY) launched the SIRAH-CoV2 initiative. We aim at providing 10-microseconds long (or longer) trajectories of coarse-grained simulations of the CoV2 protein structures reported on the PDB. Trajectories and topologies, provided as raw data in Amber format are being uploaded to the <a href="https://zenodo.org/search?page=1&size=20&q=SIRAH-CoV2&keywords=SIRAH" target="_blank">Zenodo Database</a>. Please let us know if you are interested in any particular protein, we are happy to help!</span>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.comtag:blogger.com,1999:blog-6831899316978198031.post-29583956026398139152020-03-02T10:58:00.001-08:002020-03-02T10:58:19.078-08:00SIRAH Posttranslational modifications:Best simulation of the week in JCIM!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo90fML8lxoobsdqSE5tNcler61AchsJGGBsOKSyxdTqgAMLC3SJa-42RbrfzhjxXxD2DHk9-1ybxCTx4A8viTAkwH-wdL9xpu0Di_HKKB84tbrchA1gxY4AXuxrC0duoAkFv2dNG19wf5/s1600/TOC_Garay.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="525" data-original-width="975" height="172" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo90fML8lxoobsdqSE5tNcler61AchsJGGBsOKSyxdTqgAMLC3SJa-42RbrfzhjxXxD2DHk9-1ybxCTx4A8viTAkwH-wdL9xpu0Di_HKKB84tbrchA1gxY4AXuxrC0duoAkFv2dNG19wf5/s320/TOC_Garay.tif" width="320" /></a></div>
<br />
The Journal of Chemical Information and Modelling (JCIM) selected a simulation published by <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.9b00900" target="_blank">Pablo Garay et al</a> describing posttranslational modifications in proteins within the SIRAH force field. Click <a href="https://twitter.com/JCIM_ACS/status/1233441819524026369?s=20" target="_blank">here</a> to see the video.Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-17750554133828432352020-03-02T05:47:00.001-08:002020-03-02T05:47:34.770-08:00SIRAH course: next week, University of Talca, Chile.<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZcTP5GovL1kDXy1WydNGObxNEkf8UKm6TevH9rzj447s75FUVXIrA9PNj1pNsLumSklKOnVku4fu63bwj7gTUv00kdqhy24pLEbLnTGzR01wKx1XN2vhYKYmuKz_TmQIXJwSXiJU0BhTK/s1600/FlyerTalca.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1152" data-original-width="750" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZcTP5GovL1kDXy1WydNGObxNEkf8UKm6TevH9rzj447s75FUVXIrA9PNj1pNsLumSklKOnVku4fu63bwj7gTUv00kdqhy24pLEbLnTGzR01wKx1XN2vhYKYmuKz_TmQIXJwSXiJU0BhTK/s320/FlyerTalca.jpg" width="208" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
A hands-on SIRAH course under the coordination of Dr. Horacio Poblete will be held from March 9 to 13 at the Centro de Bioinformática, Simulación y Modelado, Escuela de Ingeniería Civil en Bioinformática. Univertsity of Talca.</div>
<br />Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com2tag:blogger.com,1999:blog-6831899316978198031.post-39458411666078877562019-05-08T01:57:00.000-07:002019-05-08T01:58:45.599-07:00SIRAH lipids are ready to taste!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNgxgMtzxwfZ3DWE6AFWD9S48LGlKoJo364eNOthaI0SpQZWK6heCQn9WdwJ8askRlXxtcHAukkJwjkoN7R7RsntiDIFxJ_iu6lHhvYVbL1uD3AsU9RA5uCZZ2MtQpAMFcEjvSQZP8411x/s1600/CheeseWineWeb.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="420" data-original-width="800" height="336" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNgxgMtzxwfZ3DWE6AFWD9S48LGlKoJo364eNOthaI0SpQZWK6heCQn9WdwJ8askRlXxtcHAukkJwjkoN7R7RsntiDIFxJ_iu6lHhvYVbL1uD3AsU9RA5uCZZ2MtQpAMFcEjvSQZP8411x/s640/CheeseWineWeb.jpg" width="640" /></a></div>
<span style="font-size: large;">We just submitted a manuscript reporting the development of parameters for phospholipids. Membrane proteins simulations are remarkably accurate!
Implementations for Amber and Gromacs are available from the Download pulldown.
The preprint manuscript submitted to BioRXives by E. Barrera et al. is <a href="https://www.biorxiv.org/content/10.1101/627570v2">here.
</a></span>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com18tag:blogger.com,1999:blog-6831899316978198031.post-42383493634654755022018-10-11T07:38:00.000-07:002018-10-11T07:47:41.054-07:00SIRAH 2.0 is available to download!<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEio3ROaOpWY_cFS6_yNlnVuf4UGFAYtaKFhaG7bsM4iTiRIL_IovG-9-OWx_jkAeTv_w5RpUZyhcBxxWDNrk56EWngxGXK-qSfzlBnmacg_GNebSj38qTDOukEHy6HCiQwkxPqtxHz1JQC-/s1600/SIRAH_2.0_ready2taste.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="837" data-original-width="1600" height="332" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEio3ROaOpWY_cFS6_yNlnVuf4UGFAYtaKFhaG7bsM4iTiRIL_IovG-9-OWx_jkAeTv_w5RpUZyhcBxxWDNrk56EWngxGXK-qSfzlBnmacg_GNebSj38qTDOukEHy6HCiQwkxPqtxHz1JQC-/s640/SIRAH_2.0_ready2taste.png" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
A major update of the force field is available to download!<br />
<br />
SIRAH 2.0 is more accurate and easy to use than before. This release includes a reviewed set of bonded and non-bonded parameters for proteins, which highly improves the hydrophilic/hydrophobic balance of the residues and the conformational description of a set of structures. The mapping compatibility was expanded to GROMACS, GROMOS, CHARMM and OPLS force fields. SIRAH 2.0 also runs native on AMBER 14 or later.<br />
<br />
The preprint version of the submitted work is available at BioRxiv [<a href="https://doi.org/10.1101/436774" target="_blank">https://doi.org/10.1101/436774</a>]<br />
<br />
The SIRAH packages were renamed to include the version number describing series, year and month of release (e.g. x2_18-09 stands for SIRAH 2.0 September 2018), so users can easily check for new uploads. In a similar sense, all tutorials were updated and a FAQs document was included.Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com8tag:blogger.com,1999:blog-6831899316978198031.post-72657814894643806412018-08-16T13:30:00.000-07:002018-08-16T13:30:33.274-07:00SIRAH course at the Brazilian LNCC<b>Follow us from Aug. 20 to 24 in the <a href="http://www.lncc.br/lncc/noticias.php?idt_noticia=1271">IX School of Molecular Modeling</a> delivered at the Brazilian Petaflop center Santos Dumont</b>
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSHg611e4wwMeg-bDQdsZjqC9m-9Q9_-ueiauKezJEN7F0UyjL6hK5w3-haLgjGD8Jji-bqz8RRH6ETwadw1Jh_15S5FbS0OtBzE8NJearf8dUBh3gtcDWt-qp6YspfH0bG5TbUmpdfyaA/s1600/logo+escola+EMMSB+2018.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSHg611e4wwMeg-bDQdsZjqC9m-9Q9_-ueiauKezJEN7F0UyjL6hK5w3-haLgjGD8Jji-bqz8RRH6ETwadw1Jh_15S5FbS0OtBzE8NJearf8dUBh3gtcDWt-qp6YspfH0bG5TbUmpdfyaA/s400/logo+escola+EMMSB+2018.png" width="400" height="190" data-original-width="975" data-original-height="464" /></a></div>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-7612906458070431362018-08-01T06:35:00.000-07:002018-08-01T06:35:56.090-07:00Happy RNA day!<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyh9qWQWiSPci8J8N_yj1tP4A3fIqV-rD_7-IyQjQwnJi1ju3zcZ3nvw9Uy9SXj5JhQY5idPSy_fzTHuH5N1OToqjLN07YC7s6etP9JJd1fY-gRS1SR3xm_kdFK3YZVEZ-XWdUXNy-7AJS/s1600/RNADayJP.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyh9qWQWiSPci8J8N_yj1tP4A3fIqV-rD_7-IyQjQwnJi1ju3zcZ3nvw9Uy9SXj5JhQY5idPSy_fzTHuH5N1OToqjLN07YC7s6etP9JJd1fY-gRS1SR3xm_kdFK3YZVEZ-XWdUXNy-7AJS/s320/RNADayJP.jpg" width="320" height="219" data-original-width="1600" data-original-height="1097" /></a></div>Congratulations to the <a href="https://www.rnasociety.org">RNA community</a>!
First picture of the celebration with Juan Pablo Tosar, friend and colleague at the Institut Pasteur de Montevideo who proposed AUG 1st as the RNA day. Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-84731854033124689692018-06-08T04:51:00.000-07:002018-06-08T04:51:29.988-07:00SIRAH ff 2.0 for proteins is ready!
A significant update on the protein´s force field is ready. It is fully ported to Amber14 or newer and provides a better structural description and flexibility without changing the CG topology of individual amino acids. It will be ready to download from our site soon. Meanwhile, you can request a tarball to spantano@pasteur.edu.uy.
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrUZrbf54xqIYIcnSiT2FW69ZgqwCaCS1_5125JROJsF-GbO_GrvjKK7l4jymEInOQ3HapmmdsDZCgnWDS7hET8i5cGCQD3ssS4lozJ6srCfqUC-bEl6-TC6uId0p-oUZGrF-_nCYxAwye/s1600/FigSirah.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrUZrbf54xqIYIcnSiT2FW69ZgqwCaCS1_5125JROJsF-GbO_GrvjKK7l4jymEInOQ3HapmmdsDZCgnWDS7hET8i5cGCQD3ssS4lozJ6srCfqUC-bEl6-TC6uId0p-oUZGrF-_nCYxAwye/s320/FigSirah.jpg" width="320" height="233" data-original-width="1600" data-original-height="1164" /></a></div>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-27862828880286732462017-07-04T16:08:00.000-07:002017-07-05T11:27:40.994-07:00SIRAH Course, December 2017 - Application is Open!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHqx73PD3v73ucAUsg3MIVlY2qabRP5Byje-AjB-tq5BoYQ4vz1syFeQjoRMCIVec105B_U_PYFJNxNgdqEIoa5Qr-XzTqAWSzsTw8fsiVIrdTy1c4aTCuxQAm84n5_67vR-ZWkFB7mdNq/s1600/flyer.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="785" data-original-width="1600" height="284" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHqx73PD3v73ucAUsg3MIVlY2qabRP5Byje-AjB-tq5BoYQ4vz1syFeQjoRMCIVec105B_U_PYFJNxNgdqEIoa5Qr-XzTqAWSzsTw8fsiVIrdTy1c4aTCuxQAm84n5_67vR-ZWkFB7mdNq/s640/flyer.png" width="610" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<span style="font-family: "liberation sans" , sans-serif; font-size: large;"><span style="color: #990000;"><b>OpenLab:
Performing Molecular Simulations with SIRAH force field</b></span></span><br />
<div style="font-style: normal; font-variant: normal; margin-bottom: 0in;">
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;"><span style="font-family: "liberation sans" , sans-serif;">December</span> 11<sup style="color: black; font-weight: normal;">th</sup> to 15<sup style="color: black; font-weight: normal;">th</sup>, <b><span style="color: #990000;">2017</span></b></span></span></div>
<div style="font-style: normal; font-variant: normal; font-weight: normal; margin-bottom: 0in;">
<span style="color: black;"><span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;">Institut
Pasteur de Montevideo</span></span></span></div>
<div align="JUSTIFY" style="margin-bottom: 0in;">
<span style="font-family: "liberation sans" , sans-serif;">Montevideo, Uruguay</span><br />
<br />
<span style="font-family: "liberation sans" , sans-serif;">Thanks to the generous support of FOCEM-I<span style="font-family: "liberation sans" , sans-serif;">P Montevideo</span> (COF 03/11) we<span style="font-family: "liberation sans" , sans-serif;"> </span>will be able <span style="font-family: "liberation sans" , sans-serif;">to provide</span> full accommodation on a shared room basis, per diem and local
transportation to all participants from abroad. Travel costs must be covered by<span style="font-family: "liberation sans" , sans-serif;"> attendees' funds<span style="font-family: "liberation sans" , sans-serif;">.</span></span></span><br />
<span style="font-family: "liberation sans" , sans-serif;">There is no
registration fee.</span></div>
<div align="JUSTIFY" style="margin-bottom: 0in;">
<span style="font-family: "liberation sans" , sans-serif;"><br /></span></div>
<div align="JUSTIFY" style="font-style: normal; font-variant: normal; margin-bottom: 0in;">
<span style="font-family: "liberation sans" , sans-serif;"><span style="color: #990000; font-size: small;"><b>ORGANIZERS/TEACHING
TEAM</b></span></span></div>
<ul>
<li><span style="font-family: "liberation sans" , sans-serif;">Sergio
Pantano, PhD</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;">Matías Machado, PhD</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;"><span style="font-family: "liberation sans" , sans-serif;">Exequiel <span style="font-family: "liberation sans" , sans-serif;"><span style="font-family: "liberation sans" , sans-serif;">B</span>arrera</span></span>, PhD</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;"><span style="font-family: "liberation sans" , sans-serif;">Florencia Klein</span>, PhD Stud</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;"><span style="font-family: "liberation sans" , sans-serif;">Martin Sóñora, PhD Stud</span></span></li>
</ul>
<div align="JUSTIFY" style="margin-bottom: 0in;">
<b style="color: #990000; font-family: 'Liberation Sans', sans-serif;">VENUE</b></div>
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;">Institut
Pasteur de Montevideo, Montevideo, Uruguay [<a href="http://pasteur.edu.uy/" target="_blank"><b>website</b></a>] [<a href="https://www.google.com.uy/maps/place/Institut+Pasteur+de+Montevideo/@-34.883458,-56.118454,17z/data=%213m1%214b1%214m2%213m1%211s0x959f812a12a5ff4f:0xd495cc83077d3835?hl=es-419" target="_blank"><b>location</b></a>]</span></span><br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;">Local
facilities will allow for each student to work with an individual
computer, as well as access to a full step up to perform hands-on
practical sessions.</span></span><br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;"><br /></span></span>
<b style="color: #990000; font-family: 'Liberation Sans', sans-serif;">GENERAL
FEATURES</b><br />
<ul>
<li><span style="font-family: "liberation sans" , sans-serif;">This
OpenLab course is intended for PhD students and young research
scientists with experience in molecular dynamics simulation and a
specific problem to solve using a coarse-grained approach.</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;">10
to 15<span style="font-family: "liberation sans" , sans-serif;"> fellowships</span> will be <span style="font-family: "liberation sans" , sans-serif;">granted</span>, giving priority to those working in
South America (no selection on the basis of nationality).</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;">The
program will cover major aspects of understanding and using all
features of SIRAH force field, which include protein, <span style="font-family: "liberation sans" , sans-serif;">membrane, DNA, ions 2+,</span> and multiscale
models in explicit and implicit solvent, to address the problems
proposed by the attendees.</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;">Strong
interaction between teachers and students will be promoted through
participant's presentations, hands-on sessions and dedicated slots for
discussions on participants' research problems.</span></li>
<li><span style="font-family: "liberation sans" , sans-serif;">The language for the whole course will be English.</span></li>
</ul>
<b style="color: #990000; font-family: 'Liberation Sans', sans-serif;">HOW TO APPLY</b><span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;"> </span></span><br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;">Download the [<a href="https://drive.google.com/file/d/0B_DGe4fSMlhxZFVDdzIwM3V1OUU/view?usp=sharing" target="_blank"><b>Application Form</b></a>] and send it back in PDF format </span></span><span style="font-family: "liberation sans" , sans-serif;">to: </span><span style="color: #0b5394; font-family: "liberation sans" , sans-serif;"><b>sirahff@pasteur.edu.uy</b></span><br />
<br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="color: red; font-size: small;"><i><b>Deadline for
application is on <span style="font-family: "liberation sans" , sans-serif;">September</span> 8<sup>th</sup>, 201<span style="font-family: "liberation sans" , sans-serif;">7</span></b></i></span></span><br />
<br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;"><span style="font-family: "liberation sans" , sans-serif;">Selected<span style="font-family: "liberation sans" , sans-serif;"> participants will be notified by the e<span style="font-family: "liberation sans" , sans-serif;">nd<span style="font-family: "liberation sans" , sans-serif;"> of Septembe<span style="font-family: "liberation sans" , sans-serif;">r.</span></span></span></span></span></span></span><br />
<br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="font-size: small;">For further
information please contact: <b><span style="color: #0b5394;">sirahff@pasteur.edu.uy</span></b></span></span><br />
<br />
<span style="font-family: "liberation sans" , sans-serif;"><span style="color: #990000; font-size: small;"><b>THIS
ACTIVITY IS SUPPORTED BY</b></span></span><br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKgjvdi3eTVlkn1XMCkkwaMWbvVR43WhNhVuy38Rx9bgmByFyIPwcyjEVZsp1J596TnN9glK-IOyJJXKB8JLBoK79kkQFoVvDkC9ZgbnS7Am4vJrdiqIbNkML2egrddvltmUu6u3WT-LNm/s1600/logos.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="191" data-original-width="1158" height="65" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKgjvdi3eTVlkn1XMCkkwaMWbvVR43WhNhVuy38Rx9bgmByFyIPwcyjEVZsp1J596TnN9glK-IOyJJXKB8JLBoK79kkQFoVvDkC9ZgbnS7Am4vJrdiqIbNkML2egrddvltmUu6u3WT-LNm/s400/logos.png" width="400" /></a>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.comtag:blogger.com,1999:blog-6831899316978198031.post-51337580443463296072017-05-17T10:59:00.000-07:002017-05-17T11:01:34.081-07:00 A new publication just came out!<div class="separator" style="clear: both; text-align: left;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGYN-bczeQR_LpSZYWUUH3X_pwi5zurdWIlJoskqMZvLP7GNmlmE0CTu7QtVpoMiqNFNpzYB58Owcyw2-0_5Rk1eg5bLP2wg2gar0MG4kJtKNnIPATnBGGv-bBTy1XP_fPYXOg-enp66qx/s1600/CUTie_v6.tiff" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGYN-bczeQR_LpSZYWUUH3X_pwi5zurdWIlJoskqMZvLP7GNmlmE0CTu7QtVpoMiqNFNpzYB58Owcyw2-0_5Rk1eg5bLP2wg2gar0MG4kJtKNnIPATnBGGv-bBTy1XP_fPYXOg-enp66qx/s640/CUTie_v6.tiff" width="640" /></a></div>
<br />
We used SIRAH force field to
lead the rational design of a new generation of cAMP biosensors. This
new tool will bring huge impacts on medicine and cell biology, helping
understanding the way cAMP is distributed and regulated by proteins and
drugs.<br />
<a href="https://www.nature.com/articles/ncomms15031" rel="nofollow" target="_blank">https://www.nature.com/articles/ncomms15031</a>Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-52797794559195950492017-02-06T07:39:00.000-08:002017-02-06T07:39:22.824-08:00We've got lipids!
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1107305727 0 0 415 0;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1073743103 0 0 415 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin:0cm;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 3.0cm 70.85pt 3.0cm;
mso-header-margin:36.0pt;
mso-footer-margin:36.0pt;
mso-paper-source:0;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">We recently incorporated a series of improvements to the
gromacs version of the SIRAH force field. These include:
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-gK26xZBWDxMAPZx17FyA0OelKnsWHem8qnIZ3Hi2pDnZ6dvf174ppc15ks6PLaxmHZYIGCpElDBtzdV4Q5PHN7ykw1r2D9vmMqkMfuKayr0cZv4HEA97oA7eCfXNXLEg6X2p_1778tLi/s1600/CPP_bilayer.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="164" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-gK26xZBWDxMAPZx17FyA0OelKnsWHem8qnIZ3Hi2pDnZ6dvf174ppc15ks6PLaxmHZYIGCpElDBtzdV4Q5PHN7ykw1r2D9vmMqkMfuKayr0cZv4HEA97oA7eCfXNXLEg6X2p_1778tLi/s320/CPP_bilayer.png" width="320" /></a><span style="font-family: Arial,Helvetica,sans-serif;"><u>*Force Field Improvements</u></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>New</b>: Introducing a CG residue for lipid DMPC (dimyristoyl
phosphatidylcholine), which are named MMC.</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>New</b>: Corrections to non-bonded dna(CG)-protein(CG)
interactions</span><span style="font-family: Arial,Helvetica,sans-serif;"></span><span style="font-family: Arial,Helvetica,sans-serif;"> for sK and sR residues were added to ffnonbonded.itp (paper
in preparation)</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><u>*Misc</u></span></span>
</div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">New Folder:</span><span style="font-family: Arial,Helvetica,sans-serif;"></span><span style="font-family: Arial,Helvetica,sans-serif;"> PDB/ Repository of structures to build systems with packmol</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><u>*SIRAH tool kit</u></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">sirah_prot.map</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">New: Added support for CHARMM residue and atom naming</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><u>sirah_ions.map</u></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">New: Added support for CHARMM residue and atom naming</span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><u>sirah_lipid.map</u></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">
</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">New map file for lipids including mapping files for DMPC (MMC). </span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Download the latest version!</span></span></div>
<div class="MsoNormal">
<br /></div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-56487077651000556842016-12-13T04:01:00.001-08:002016-12-13T06:12:11.521-08:00Welcome Exequiel!<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1107305727 0 0 415 0;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1073743103 0 0 415 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin:0cm;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 3.0cm 70.85pt 3.0cm;
mso-header-margin:36.0pt;
mso-footer-margin:36.0pt;
mso-paper-source:0;}
div.WordSection1
{page:WordSection1;}
</style>
-->
<span style="font-family: "cambria"; font-size: 12.0pt;">The
SIRAH team welcomes Exequiel Barrera, who is starting his PostDoc in the group
thanks to the CONICET-Intitut Pasteur Agreement. Exequiel is developing
Coarse-Grained phospholipids within the SIRAH force field. The first set of
parameters for DMPC have been published in <a href="http://onlinelibrary.wiley.com/doi/10.1002/psc.2934/abstract" target="_blank">Astrada et al.</a> and will be available
soon!</span><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMgwEONMExtDM0zo1NLR_VGaZNcRTsMXt9oet_9AyYKY62uyVXDLwdtqukdQaWOtQs16QfD_oJ6tVkYA25ZaDK1aVW_DxOWkyAvZ7M5uSFRRA0MUIoDHo8CUVdGTMcQklhLr82mX5dIijv/s1600/IMG_20161017_152708004.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMgwEONMExtDM0zo1NLR_VGaZNcRTsMXt9oet_9AyYKY62uyVXDLwdtqukdQaWOtQs16QfD_oJ6tVkYA25ZaDK1aVW_DxOWkyAvZ7M5uSFRRA0MUIoDHo8CUVdGTMcQklhLr82mX5dIijv/s320/IMG_20161017_152708004.jpg" width="320" /></a></div>
<span style="font-family: "cambria"; font-size: 12.0pt;"> </span>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com1tag:blogger.com,1999:blog-6831899316978198031.post-69076945913131378542016-11-29T09:24:00.000-08:002016-11-29T09:24:19.049-08:00Welcome Florencia!
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1073743103 0 0 415 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin:0cm;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 3.0cm 70.85pt 3.0cm;
mso-header-margin:36.0pt;
mso-footer-margin:36.0pt;
mso-paper-source:0;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<br />
<div class="MsoNormal" style="margin-left: 18.0pt;">
The SIRAH team welcomes Florencia
Klein, who is starting her PhD in our group working on design of fluorescent
sensors and modeling of cAMP nanocompartments.</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlJN9WSqFqPJmxB-Lx4Du5tPR3bJT9qq7unCrlI1Tb6tiEpq7PfaVNq2Cofj2KeJ9sG2c2I-oA__I657rGXd5Su7KV0BCptLHulH3aui92gYzETqPtzkLHsDko2gL1hkB8uTElB1k3pyCo/s1600/FKlein-SIRAH.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlJN9WSqFqPJmxB-Lx4Du5tPR3bJT9qq7unCrlI1Tb6tiEpq7PfaVNq2Cofj2KeJ9sG2c2I-oA__I657rGXd5Su7KV0BCptLHulH3aui92gYzETqPtzkLHsDko2gL1hkB8uTElB1k3pyCo/s320/FKlein-SIRAH.jpg" width="320" /></a></div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-80197133261503243082016-10-17T11:14:00.001-07:002016-10-17T11:15:10.852-07:00The Coarse-Grained SIRAH force field now includes Calcium ions!<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:"MS 明朝";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:-536870145 1073743103 0 0 415 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin:0cm;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;
mso-ansi-language:EN-GB;}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
font-family:Cambria;
mso-ascii-font-family:Cambria;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"MS 明朝";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Cambria;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:"Times New Roman";
mso-bidi-theme-font:minor-bidi;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 3.0cm 70.85pt 3.0cm;
mso-header-margin:36.0pt;
mso-footer-margin:36.0pt;
mso-paper-source:0;}
div.WordSection1
{page:WordSection1;}
</style>
-->
<span lang="EN-GB" style="font-family: "cambria"; font-size: 12.0pt;">We recently incorporated parameters to simulate
Ca2+ ions in a fully unbiased fashion. vdW parameters are set in such a way
that a large radius is used to interact with solvent, while Calcium-protein
contacts are calculated with a smaller size. This allows negative moieties to
coordinate Ca2+ mostly because of electrostatic stabilization and without
imposing specific constraints. Use of these parameters in a Calmodulin system
helped to rationalize the effect of an Ataxia-related point mutation in PMCA3
(<a href="http://dx.doi.org/10.1016/j.bbadis.2016.09.007" target="_blank">click here to see the publication</a>).</span><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8PGpQ52IRRdwHZeiH30d8Q6IumSpMbQBwT_1Js0JS-7GazBI4mqxBXnAMcLEevA8579TgBqYYE34TDFoagqAB5m50OuzT7f3tRZugO0Nw_mEVJuw3X-_PzKLh4PoGjQcdWYM9ORB5jviO/s1600/CaMCa2%252B.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="208" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8PGpQ52IRRdwHZeiH30d8Q6IumSpMbQBwT_1Js0JS-7GazBI4mqxBXnAMcLEevA8579TgBqYYE34TDFoagqAB5m50OuzT7f3tRZugO0Nw_mEVJuw3X-_PzKLh4PoGjQcdWYM9ORB5jviO/s320/CaMCa2%252B.gif" width="320" /></a></div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-61069608431637622052016-03-10T05:59:00.000-08:002016-03-10T05:59:11.665-08:00Latest Update: Circular DNAWe have recently added the possibility to simulate circular DNA using implicit (Amber) and explicit (Gromacs) solvent. Check out the tutorial's pull-down. <br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIPakOmfdBJlm5iPX8pweokQmV1T4lVsOlFFDrR5Z-cIaKeoTFOAryvG_inP-pMSo999L3LVwOrFmWHTssQ0f8WASTN1QFL2aqVAhEEES3LuRSjSCUbmQOVW_OBXzELHjBHYiRDtyi0IXo/s1600/ccdna2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="269" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIPakOmfdBJlm5iPX8pweokQmV1T4lVsOlFFDrR5Z-cIaKeoTFOAryvG_inP-pMSo999L3LVwOrFmWHTssQ0f8WASTN1QFL2aqVAhEEES3LuRSjSCUbmQOVW_OBXzELHjBHYiRDtyi0IXo/s320/ccdna2.jpg" width="320" /></a></div>
<br />Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-28221026112967252522016-02-29T06:58:00.000-08:002016-02-29T06:59:43.938-08:00Protein Biophysics at the End of the World<div style="text-align: justify;">
<a href="http://www.ciencias.uchile.cl/ciencias/labbq/minisymposium/#slide1" target="_blank"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: large;">Check out this biophysics meeting in Chile. Fellowships available!</span></span></a></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.ciencias.uchile.cl/ciencias/labbq/minisymposium/#slide1" target="_blank"><img alt="http://www.ciencias.uchile.cl/ciencias/labbq/minisymposium/#slide1" border="0" height="191" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglYMdsEr9ojPnbCG_JAsujPt5SpadmE2HI_bTX-m4_chj8evVFXDKxPVgmBqJFpkGhf6wsfVfg2TFAUWfLAMwKEahRgJFJcBe8fgmUPLoqyJ2xRKq157CI9qcG_S4K6Xwhx8eA42a13we5/s320/ProtEndOfTheWorld.jpg" width="320" /></a></div>
<br />
<br />Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-54604119597982473232015-12-07T11:48:00.000-08:002016-01-15T07:55:22.332-08:00Introducing SIRAH Tools!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi34DcCiFGzvqBM0GUwOmSzdJ76ymTejDQLKeiGuZtilkvBS4yWfCKGyLKj7ja9d5F8hyphenhyphen6byH2VJlT4vxGIsCAHgizLPCnKhL_krXvngjzUSLXx7kqRVps0kPYYeOYNcOCv5B8lvkCgf0tR/s1600/sirahpackage.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="202" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi34DcCiFGzvqBM0GUwOmSzdJ76ymTejDQLKeiGuZtilkvBS4yWfCKGyLKj7ja9d5F8hyphenhyphen6byH2VJlT4vxGIsCAHgizLPCnKhL_krXvngjzUSLXx7kqRVps0kPYYeOYNcOCv5B8lvkCgf0tR/s320/sirahpackage.png" width="320" /></a></div>
<br />
<div class="MsoNormal">
We published a manuscript in Bioinformaics <a href="http://bioinformatics.oxfordjournals.org/content/early/2016/01/14/bioinformatics.btw020.abstract?keytype=ref&ijkey=Z0zUPyOkxCfRJgr" target="_blank">[link to article]</a> presenting a set of utilities
to:</div>
<div class="MsoNormal">
<ul>
<li>Easily convert atomistic coordinates to residue-based CG
schemes</li>
<li>Write GROMACS’ topologies at arbitrary level of resolution into PSF format</li>
<li>A Tcl plugin for VMD to visualize, analyze and retrieve
pseudo-atomistic information (backmap) from CG trajectories performed with the SIRAH
force field.</li>
</ul>
<ul>
</ul>
</div>
<div class="MsoNormal">
</div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com0tag:blogger.com,1999:blog-6831899316978198031.post-91496171676080029762015-03-02T07:47:00.000-08:002015-03-26T09:25:00.776-07:00UNESCO auspices the SIRAH course 2015!<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic14UgaimrB286iaQ7CpPQwKuJfhjy3PCce3YR3rO8-iUVYf-U9iQ1AiWksT2MVeKkWdcAw6IVxNSb79Sz1IgycWOhk13GLxr58DU1dNQUlHhppdioPYieUVQvM4ZoTfu265sN9w-5TXEC/s1600/flyer.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic14UgaimrB286iaQ7CpPQwKuJfhjy3PCce3YR3rO8-iUVYf-U9iQ1AiWksT2MVeKkWdcAw6IVxNSb79Sz1IgycWOhk13GLxr58DU1dNQUlHhppdioPYieUVQvM4ZoTfu265sN9w-5TXEC/s1600/flyer.png" height="422" width="640" /></a></div>
<br />
We thank the authorities of UNESCO for supporting the OpenLab: Performing Molecular Simulations with SIRAH force field<br />
<a name='more'></a><br />
We encourage students to participate. There are just two weeks left for application! Go to the following link for more information [<a href="http://www.sirahff.com/2014/11/sirah-course-may-2015-application-is.html">SIRAH course 2015</a>]Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.comtag:blogger.com,1999:blog-6831899316978198031.post-30183312326380339772015-02-10T08:39:00.000-08:002015-04-14T08:38:37.968-07:00The SIRAH Force Field is the cover image of the new JCTC issue!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8NjlD8x-K0rlYvVu2arpkbBtnIDSZUOUkZSJufWfc5PhITKsEw20DCMXvvKIQSXd9TnO0oZp4EiY-HmeqKKjgOFxFAEAOM81jieAAVj-RMQhrOawC9WA8kn1bPKQ23_ljdl5XIZBcbYMG/s1600/jctcce.2015.11.issue-2.cover.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8NjlD8x-K0rlYvVu2arpkbBtnIDSZUOUkZSJufWfc5PhITKsEw20DCMXvvKIQSXd9TnO0oZp4EiY-HmeqKKjgOFxFAEAOM81jieAAVj-RMQhrOawC9WA8kn1bPKQ23_ljdl5XIZBcbYMG/s1600/jctcce.2015.11.issue-2.cover.jpg" height="320" width="240" /></a></div>
<div style="text-align: justify;">
The development of coarse-grained models that reduce the computational cost keeping the essential interactions ruling molecular systems is experiencing an enormous expansion.</div>
<div style="text-align: justify;">
<br />
Facilitating the use of these models outside the small developer's community is one of the challenges in this field. We present the SIRAH force field for proteins, which completes a set of parameters for coarse-grained and multiresolution simulation of biomolecular systems using a standard MD Hamiltonian, making its use straightforward in popular simulation packages. See L. Darré, M. R. Machado, A. F. Brandner, H. C. González, S. Ferreira, and S. Pantano, pp 723–739.</div>
<div style="text-align: justify;">
[<a href="http://pubs.acs.org/doi/abs/10.1021/ct5007746" target="_blank">Link to Article</a>] [<a href="http://pubs.acs.org/action/showLargeCover?jcode=jctcce&vol=11&issue=2" target="_blank">Link to Issue</a>]</div>
Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.comtag:blogger.com,1999:blog-6831899316978198031.post-36224024863868965612015-01-23T06:59:00.001-08:002015-01-23T07:12:05.283-08:00International call for postdoctoral positions <div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOwUk93EoktzOL3FQkYibZ8mxCFxPM9fPrNyU1ajKXXIPxW7xUvM9KaDElSUMltGwoz1Q9rvPboW9am3ZnrCCLc93fnFg6ro315H6np65rBVb8y7ZOlDOyX4rLNUMqbK1kzzk1JE21Wvry/s1600/Calmette.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOwUk93EoktzOL3FQkYibZ8mxCFxPM9fPrNyU1ajKXXIPxW7xUvM9KaDElSUMltGwoz1Q9rvPboW9am3ZnrCCLc93fnFg6ro315H6np65rBVb8y7ZOlDOyX4rLNUMqbK1kzzk1JE21Wvry/s1600/Calmette.jpg" height="261" width="320" /></a></div>
<div style="text-align: justify;">
There is an international open call to apply for postdoctoral positions (Calmette and Yersin Program) funded by the International Affairs Department of the Institut Pasteur International Network. <br />
We are looking for applicants to develop research projects in biomolecular simulations using <br />
SIRAH at the Institut Pasteur de Montevideo. <br />
The fellowships include a fixed-term local contract with social charges for a duration of 2 years covering living expenses, insurance and a return air ticket per year. <b>Application deadline for postdoctoral Program: May 31th, 2015</b>. See all the information and eligibility criteria <a href="http://www.pasteur.fr/en/international/international-network-courses/fellowships/postdoctoral-grants">here.</a><br />
Interested persons should contact Sergio Pantano (spantano "at" pasteur.edu.uy) <b>before April 30</b> to discuss about different projects available.</div>
<br />Sirah ForceFieldhttp://www.blogger.com/profile/08331566684029128028noreply@blogger.com