Zobrazeno 1 - 10
of 31
pro vyhledávání: '"Andreas F. Tillack"'
Publikováno v:
QRB Discovery, Vol 3 (2022)
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular H-bonds. A
Externí odkaz:
https://doaj.org/article/6b6ac81b42d749f1ab07da43cc3aeb94
Autor:
Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Leonardo Solis-Vasquez, Stefano Forli
Publikováno v:
Parallel Comput
Irregular applications can be found in different scientific fields. In computer-aided drug design, molecular docking simulations play an important role in finding promising drug candidates. AutoDock is a software application widely used for predictin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e2c61e1d4e106d89a85cbd1cc34de14
https://pubmed.ncbi.nlm.nih.gov/34898769
https://pubmed.ncbi.nlm.nih.gov/34898769
Autor:
Scott LeGrand, Mathialakan Thavappiragasam, Jens Glaser, Andreas F. Tillack, Matthew B. Baker, Oscar Hernandez, Josh V. Vermaas, Aaron Scheinberg, David M. Rogers, Ada Sedova, Jeff Larkin, Swen Boehm
Publikováno v:
The International Journal of High Performance Computing Applications. 35:452-468
Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit supercomputer
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9a79c7febfe5a67c8e4436b62f2cd6d3
https://doi.org/10.1177/10943420211001565
https://doi.org/10.1177/10943420211001565
Autor:
Lewis E. Johnson, Bruce H. Robinson, Stephanie J. Benight, Delwin L. Elder, Scott R. Hammond, Andreas F. Tillack, Wolfgang Heni, Larry R. Dalton
Publikováno v:
Physical Chemistry of Semiconductor Materials and Interfaces XX.
Hybrid organic electro-optic (OEO) devices consist of a layer of ordered organic chromophores confined between layers of metals or semiconductors, enabling optical fields to be tightly confined within the OEO material. The combination of tight confin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::970e2e2d8b4e1c2ae12e8dee7d1c3136
https://doi.org/10.1117/12.2594939
https://doi.org/10.1117/12.2594939
Autor:
Sapana V. Shedge, Aleksey A. Kocherzhenko, Christine M. Isborn, Andreas F. Tillack, Jessica Maat, Lewis E. Johnson, Xochitl A. Sosa Vazquez, Jacob Wilmer
Publikováno v:
The Journal of Physical Chemistry C. 123:13818-13836
Excitonic interactions often significantly affect the optoelectronic properties of molecular materials. However, their role in determining the nonlinear optical response of organic electro-optic materials remains poorly understood. In this paper, we
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2a82326e3051ab27d33adbdcb9cc45e2
https://doi.org/10.1021/acs.jpcc.8b12445
https://doi.org/10.1021/acs.jpcc.8b12445
Autor:
Andreas Koch, Stefano Forli, Leonardo Solis-Vasquez, Diogo Santos-Martins, Michel F. Sanner, Andreas F. Tillack
Publikováno v:
J Chem Theory Comput
AutoDock4 is a widely used program for docking small molecules to macromolecular targets. It describes ligand-receptor interactions using a physics-inspired scoring function that has been proven useful in a variety of drug discovery projects. However
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ad42ef0344c5bd2f9e6f015803ef48ef
https://pubmed.ncbi.nlm.nih.gov/33403848
https://pubmed.ncbi.nlm.nih.gov/33403848
Autor:
Jerome Eberhardt, Diogo Santos-Martins, Andreas Koch, Andreas F. Tillack, Leonardo Solis-Vasquez, Stefano Forli
Publikováno v:
IA3@SC
AUTODOCK is a molecular docking software widely used in computational drug design. Its time-consuming executions have motivated the development of AUTODOCK-GPU, an OpenCL-accelerated version that can run on GPUs and CPUs. This work discusses the deve
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0872b0f91b0721d223222716a45800c1
https://doi.org/10.1109/ia351965.2020.00008
https://doi.org/10.1109/ia351965.2020.00008
Autor:
Mathialakan Thavappiragasam, Oscar Hernandez, Josh V. Vermaas, Aaron Scheinberg, Ada Sedova, Andreas Koch, Duncan Poole, Jeremy C. Smith, Leonardo Solis-Vasquez, Stefano Forli, Andreas F. Tillack, Rupesh Agarwal, Scott LeGrand, Diogo Santos-Martins, Jeff Larkin
Publikováno v:
ArXiv
BCB
BCB
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d7295f3947b6aac2db3e726b822acd49
https://europepmc.org/articles/PMC7359529/
https://europepmc.org/articles/PMC7359529/
Autor:
Dmytro Bykov, Ramanan Sankaran, K. C. Gottiparthi, Shirin Faraji, Lucas Visscher, J. C. Oefelein, O. E. B. Messer, Matthew R. Norman, Andreas F. Tillack, C. de Graaf, R. K. Kathir, T. P. Straatsma, M. Wibowo, Lixiang Luo, W. Joubert, A. L. Barnes, Remco W. A. Havenith, J. A. Harris, E. F. D'Azevedo, Y. W. Li, H. J. Aa. Jensen, Jack C. Wells, L. E. Aguilar Suarez, Jeffrey M. Larkin, Ria Broer, D. I. Lyakh
Publikováno v:
Luo, L, Straatsma, T P, Suarez, L E A, Broer, R, Bykov, D, D'Azevedo, E F, Faraji, S S, Gottiparthi, K C, De Graaf, C, Harris, J A, Havenith, R W A, Jensen, H J A, Joubert, W, Kathir, R K, Larkin, J, Li, Y W, Lyakh, D I, Messer, O E B, Norman, M R, Oefelein, J C, Sankaran, R, Tillack, A F, Barnes, A L, Visscher, L, Wells, J C & Wibowo, M 2020, ' Pre-exascale accelerated application development : The ORNL Summit experience ', IBM Journal of Research and Development, vol. 64, no. 3-4, 8960361 . https://doi.org/10.1147/JRD.2020.2965881
IBM Journal of Research and Development, 64(3/4):8960361, 11:1-11:21. IBM Corporation
Ibm journal of research and development, 64(3-4):8960361. IBM CORP
Luo, L, Straatsma, T P, Suarez, L E A, Broer, R, Bykov, D, D'Azevedo, E F, Faraji, S S, Gottiparthi, K C, De Graaf, C, Harris, J A, Havenith, R W A, Jensen, H J A, Joubert, W, Kathir, R K, Larkin, J, Li, Y W, Lyakh, D I, Messer, O E B, Norman, M R, Oefelein, J C, Sankaran, R, Tillack, A F, Barnes, A L, Visscher, L, Wells, J C & Wibowo, M 2020, ' Pre-exascale accelerated application development : The ORNL Summit experience ', IBM Journal of Research and Development, vol. 64, no. 3/4, 8960361, pp. 11:1-11:21 . https://doi.org/10.1147/JRD.2020.2965881
IBM Journal of Research and Development, 64(3/4):8960361, 11:1-11:21. IBM Corporation
Ibm journal of research and development, 64(3-4):8960361. IBM CORP
Luo, L, Straatsma, T P, Suarez, L E A, Broer, R, Bykov, D, D'Azevedo, E F, Faraji, S S, Gottiparthi, K C, De Graaf, C, Harris, J A, Havenith, R W A, Jensen, H J A, Joubert, W, Kathir, R K, Larkin, J, Li, Y W, Lyakh, D I, Messer, O E B, Norman, M R, Oefelein, J C, Sankaran, R, Tillack, A F, Barnes, A L, Visscher, L, Wells, J C & Wibowo, M 2020, ' Pre-exascale accelerated application development : The ORNL Summit experience ', IBM Journal of Research and Development, vol. 64, no. 3/4, 8960361, pp. 11:1-11:21 . https://doi.org/10.1147/JRD.2020.2965881
High-performance computing (HPC) increasingly relies on heterogeneous architectures to achieve higher performance. In the Oak Ridge Leadership Facility (OLCF), Oak Ridge, TN, USA, this trend continues as its latest supercomputer, Summit, entered prod
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c2203be5ee46d879f2e3531e1e392f2
https://hdl.handle.net/11370/deba9925-91d6-42be-94ba-a4a1596c9c19
https://hdl.handle.net/11370/deba9925-91d6-42be-94ba-a4a1596c9c19
Autor:
Mathialakan Thavappiragasam, Gilchan Park, Kendall G. Byler, Leighton Coates, Laura Zanetti-Polzi, Jeffrey M. Larkin, Junqi Yin, John A. Gunnels, Omar Demerdash, Loukas Petridis, Ada Sedova, Carlos Soto, Aaron Scheinberg, Mai Zahran, Scott LeGrand, Jens Glaser, Jerome Baudry, Stephan Irle, Samuel Yen-Chi Chen, Andrey Kovalevsky, Isabella Daidone, Julie C. Mitchell, Arvind Ramanathan, Connor J. Cooper, Duncan Poole, V. Q. Vuong, Diogo Santos-Martins, David M. Rogers, Shinjae Yoo, Y. Shen, Oscar Hernandez, A. Tsaris, Swen Boehm, Debsindhu Bhowmik, Travis J Lawrence, Daniel W. Kneller, Shih-Hsien Liu, Jeremy C. Smith, Line Pouchard, Matthew B. Baker, Stefano Forli, Sally R. Ellingson, Anna Pavlova, Rupesh Agarwal, Micholas Dean Smith, Atanu Acharya, James C. Gumbart, Andreas F. Tillack, John D. Eblen, Josh V. Vermaas, Jerry M. Parks
Publikováno v:
Journal of chemical information and modeling 60 (2020): 5832–5852. doi:10.1021/acs.jcim.0c01010
info:cnr-pdr/source/autori:Acharya A.; Agarwal R.; Baker M.B.; Baudry J.; Bhowmik D.; Boehm S.; Byler K.G.; Chen S.Y.; Coates L.; Cooper C.J.; Demerdash O.; Daidone I.; Eblen J.D.; Ellingson S.; Forli S.; Glaser J.; Gumbart J.C.; Gunnels J.; Hernandez O.; Irle S.; Kneller D.W.; Kovalevsky A.; Larkin J.; Lawrence T.J.; Legrand S.; Liu S.-H.; Mitchell J.C.; Park G.; Parks J.M.; Pavlova A.; Petridis L.; Poole D.; Pouchard L.; Ramanathan A.; Rogers D.M.; Santos-Martins D.; Scheinberg A.; Sedova A.; Shen Y.; Smith J.C.; Smith M.D.; Soto C.; Tsaris A.; Thavappiragasam M.; Tillack A.F.; Vermaas J.V.; Vuong V.Q.; Yin J.; Yoo S.; Zahran M.; Zanetti-Polzi L./titolo:Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19/doi:10.1021%2Facs.jcim.0c01010/rivista:Journal of chemical information and modeling/anno:2020/pagina_da:5832/pagina_a:5852/intervallo_pagine:5832–5852/volume:60
Journal of Chemical Information and Modeling
ChemRxiv
article-version (number) 1
article-version (status) pre
info:cnr-pdr/source/autori:Acharya A.; Agarwal R.; Baker M.B.; Baudry J.; Bhowmik D.; Boehm S.; Byler K.G.; Chen S.Y.; Coates L.; Cooper C.J.; Demerdash O.; Daidone I.; Eblen J.D.; Ellingson S.; Forli S.; Glaser J.; Gumbart J.C.; Gunnels J.; Hernandez O.; Irle S.; Kneller D.W.; Kovalevsky A.; Larkin J.; Lawrence T.J.; Legrand S.; Liu S.-H.; Mitchell J.C.; Park G.; Parks J.M.; Pavlova A.; Petridis L.; Poole D.; Pouchard L.; Ramanathan A.; Rogers D.M.; Santos-Martins D.; Scheinberg A.; Sedova A.; Shen Y.; Smith J.C.; Smith M.D.; Soto C.; Tsaris A.; Thavappiragasam M.; Tillack A.F.; Vermaas J.V.; Vuong V.Q.; Yin J.; Yoo S.; Zahran M.; Zanetti-Polzi L./titolo:Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19/doi:10.1021%2Facs.jcim.0c01010/rivista:Journal of chemical information and modeling/anno:2020/pagina_da:5832/pagina_a:5852/intervallo_pagine:5832–5852/volume:60
Journal of Chemical Information and Modeling
ChemRxiv
article-version (number) 1
article-version (status) pre
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79326e7712c0be5402b46e8c6ef2b9fd