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Lead optimization mapper: automating free energy calculations for lead optimization

Shuai Liu, Yujie Wu, Teng Lin, Robert Abel, Jonathan P. Redmann, Christopher M. Summa, Vivian R. Jaber, Nathan M. Lim, David L. Mobley
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy Supporting Information In the Supporting Information, we provide .mol2 files for the FXa, trypsin, fragment, and SAMPL3 test
more &raquo; ... sets, as well as graphs automatically constructed by LOMAP for these sets, with edges labeled by the corresponding trimmed maximum common substructures. We also provide details of the origins of the trypsin test set, and a figure of compound pairs selected at random from the fragment set. Supporting information is available through the journal, and supporting files are available at ttp://mobleylab.org/ paper_support/LOMAP SI.tar.gz}.%\bibliograpystyleieetr NIH Public Access calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license.
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Making Do with More: The Next Generation Workflow Explored

<span title="">2014</span> <i title="Society of Motion Picture and Television Engineers (SMPTE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5wvetaxl3zdi5jjvqhidqayrke" style="color: black;">SMPTE Motion Imaging Journal</a> </i> &nbsp;
USA ing Digital Identification, LLC (Ad-ID), USA); Clyde Smith (Fox Networks <p pp lagpeliarsisaane .  ...  Systems Consulting, USA) Industry Luncheon ne Chin Chye Koh (Nevion, USA) Audio Part 2 Networked Media in the Facility Part 2 September 2014 SMPTE Motion Imaaing Journal // 9 OA A “> UIC ATi William Redmann  ... 
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Page 828 of Psychological Abstracts Vol. 93, Issue 2 [page]

<span title="">2006</span> <i title="American Psychological Association"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_psychological-abstracts" style="color: black;">Psychological Abstracts </a> </i> &nbsp;
., 5266 Redmann, Christopher P., 3637 Reece, Sarah E., 3483 Reed, Pamela G., 5219 Reeder, Glenn D., 4184 Reeves, Jenny, 5718 Reeves, Scott, 5557, 5558, 5577 Rehm, Roberta, 3996 Reich, John W., 4240 Reich  ...  Scott, 4847 Richards, P.  ... 
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2014 Annual Technical Conference Program

<span title="">2014</span> <i title="Society of Motion Picture and Television Engineers (SMPTE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5wvetaxl3zdi5jjvqhidqayrke" style="color: black;">SMPTE Motion Imaging Journal</a> </i> &nbsp;
Lennon (MediAnswers, USA Bruce Devlin (Dalet, U.K.); Simon Adler (Dalet, USA) Drew Lanham (Nexidia, USA) Juan Jose Anaya (SAPEC, Spain); Damian Ruiz (Universitat P de Valéncia, Spain) October 2014 SMPTE  ...  The techniques and developments described will propel the suspension of disbelief" that is at the center of the cinema experience Charies Robinson and Nicolas Tsingos (Dolby Laboratories, USA) William Redmann  ... 
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Page 599 of Bulletin of the History of Medicine Vol. 31, Issue 6 [page]

<i title="Johns Hopkins University Press"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_bulletin-of-the-history-of-medicine" style="color: black;">Bulletin of the History of Medicine</a> </i> &nbsp;
., 34 Riese, Walther, 291-292, 294 Riesman, David, 499 Ritter, 173 Robin, 175 Robinson, Christopher, 392 Robinson, Gregory, 28 Robinson, John, 392 Robinson, Victor, 167 Roche, P 4 C, 238 Rogers, Fred B  ...  Subba, 379 Redmann, 35 Reed, Walter, 242, 279, 280 Reeve, Peter, 144 Renzi, S. de, 103 Rhazes, 210, 312, 316, 428, 432, 433 Richter, A.  ... 
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ONLINE PROBLEM POSING UNTUK MENINGKATKAN KEMAMPUAN MEMAHAMI MATERI BERBAHASA INGGRIS PADA PERKULIAHAN BILINGUAL MAHASISWA JURUSAN PENDIDIKAN MATEMATIKA RKBI UNIVERSITAS PENDIDIKAN GANESHA

Ni Made Sri Mertasari
<span title="2013-04-01">2013</span> <i title="Universitas Pendidikan Ganesha"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xm5yhbezafe3fpga5772lrk7am" style="color: black;">JPI (Jurnal Pendidikan Indonesia)</a> </i> &nbsp;
Selama proses uji coba, portal web e-learning yang sudah dikembangkan dijalankan di web server IBM System X3650, P III Xeon 4 CPU 2Ghz, memory 2 GB.  ...  Selain itu, isu utama untuk mengintegrasikan teknologi ke dalam pembalajaran adalah akses ke teknologi dan kendala memanfaatkan teknologi tersebut (Kotrlik & Redmann, 2009).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.23887/jpi-undiksha.v2i1.1412">doi:10.23887/jpi-undiksha.v2i1.1412</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kjbcl6d5gfct7i5liuendmlphq">fatcat:kjbcl6d5gfct7i5liuendmlphq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720195228/https://ejournal.undiksha.ac.id/index.php/JPI/article/download/1412/1273" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/99/32/99320e5b5b2ac427230c31d2eb9ebce3cbc285a9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.23887/jpi-undiksha.v2i1.1412"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Personalia 2009

K. Majewski
<span title="2009-12-01">2009</span> <i title="University of Wisconsin Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mxna42rb7jghdfdybk52dkd3gm" style="color: black;">Monatshefte</a> </i> &nbsp;
P.: Todd Presner, Ph.D Christopher M. Stevens, Ph.D Christopher Wild, Ph.D. (Iv) Christine Kanz, Ph.D. (U TX Austin) Magdalena A. Tarnawska, Ph.D. (U OK) Ehrhard Bahr, Ph.D. Franz H. Bauml, Ph.D.  ...  P.: Dorian Roehrs, Ph.D. Siegfried Mews, Ph.D. Christoph Daniel Weber, Ph.D. Christoph E. Schweitzer, Ph.D. (U WI Madison) Sidney R. Smith, Ph.D. Sr. Lect.: Carmen Terry, M.A. Petrus W. Tax. Ph.D.  ... 
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Plant species dominance shifts across erosion edge–meadow transects in the Swiss Alps

Corinne Huck, Christian Körner, Erika Hiltbrunner
<span title="2013-01-22">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wp44aeqzsjczzjdae2l7vu7q5i" style="color: black;">Oecologia</a> </i> &nbsp;
We are grateful to Christophe Bornand for his ideas and for reading a previous version of this manuscript.  ...  Differences are statistically significant at: ***p \ 0.001; **p \ 0.01; *p \ 0.05.  ...  high demands for a factor (***p \ 0.001; **p \ 0.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00442-012-2583-6">doi:10.1007/s00442-012-2583-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23337968">pmid:23337968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kuk35wdxmnhnnowgoodhwwbzau">fatcat:kuk35wdxmnhnnowgoodhwwbzau</a> </span>
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Personalia 2007

Kristopher Imbrigotta
<span title="">2007</span> <i title="University of Wisconsin Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mxna42rb7jghdfdybk52dkd3gm" style="color: black;">Monatshefte</a> </i> &nbsp;
P.: Lect.: Instr. Emer.: Kalamazoo College Kalamazoo, MI 49006-3295 (G B) Asso. P.: Joseph L. Brockington, Ph.D. Jennifer Redmann, Ph.D.* Michael J. Sosulski, Ph.D Hardy Fuchs, Ph.D. Joe K.  ...  P.: Heidi Schlipphacke, Ph.D. Ulrich Schénherr, Ph.D. Asst. P.: Christopher Pavsek, Ph.D.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1353/mon.2008.0000">doi:10.1353/mon.2008.0000</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3vfdfyzu7fcexmrvwum2hltaxi">fatcat:3vfdfyzu7fcexmrvwum2hltaxi</a> </span>
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Personalia 2011

<span title="2011-12-01">2011</span> <i title="University of Wisconsin Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mxna42rb7jghdfdybk52dkd3gm" style="color: black;">Monatshefte</a> </i> &nbsp;
(lv 1) Vincent Louis VanderHeijden, Ph.D Hubert P. Heinen, Ph.D. Robert D. King, Ph.D. J. Christopher Middleton, Dr. phil. Hans-Bernhard Moeller, Ph.D. Robert R. Mollenauer, Ph.D. Thomas J.  ...  Johan P. Snapper, Ph.D. Frederic C. Tubach, Ph.D.  ... 
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Sexual Risk Behavior In Men Attending Mardi Gras Celebrations In New Orleans, Louisiana

Eric G. Benotsch, Christopher D. Nettles, Felicia Wong, Jean Redmann, Jill Boschini, Steven D. Pinkerton, Kathleen Ragsdale, John J. Mikytuck
<span title="2007-06-01">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zdzyszeyrc6flp6lm3fuu6meq" style="color: black;">Journal of community health</a> </i> &nbsp;
receptive anal sex acts (rho = −0.29, p < .01), and fewer unprotected receptive anal partners (rho = −0.29, p < .01).  ...  The overall model was significant, χ 2 (4, N = 112) = 11.20, p < .05.  ... 
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Page 206 of Psychological Abstracts Vol. 93, Issue Index [page]

<i title="American Psychological Association"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_psychological-abstracts" style="color: black;">Psychological Abstracts </a> </i> &nbsp;
, Christopher P., 3637 Redmond, Alyssa, 28086 Redmond, Brian, 30640 Redmond, Cleve, 8258, 29825 Redshaw, Maggie, 22992, 25515 Redwin, Robert, 22899 Ree, Malcolm James, 12599 Reebye, Pratibha, 17404, 26055  ...  22301 Redman, Jennifer, 20008 Redman, Jessica, 10065 Redman, Peggy Deal, 21172 Redman, Peter, 9912 Redman, Richar W., 5409 Redman, Richard W., 5266, 33231 Redman, Richard, 29858 Redman, Tom, 21331, 24357 Redmann  ... 
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Page 1925 of Mathematical Reviews Vol. , Issue Index [page]

<i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Volaufova, Julia (with Redmann, Stephen M., Jr.; LaMotte, Lynn R.) Is logistic regression the best for binomial response? (English summary) Vrontos, I. D.  ...  Skrondal, Anders (with Rabe-Hesketh, Sophia) * Generalized latent variable modeling. 2004m:62009 Small, Christopher G.  ... 
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Personalia 2008

<span title="2008-12-01">2008</span> <i title="University of Wisconsin Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mxna42rb7jghdfdybk52dkd3gm" style="color: black;">Monatshefte</a> </i> &nbsp;
P.: Joseph L. Brockington, Ph.D Jennifer Redmann, Ph.D. (lv 2.3) Michael J. Sosulski, Ph.D Hardy Fuchs, Ph.D. Joe K.  ...  P.: Retired BT:2 BR:28 *Marshall University Huntington, WV 25755-2652 (L B) Prof.: Christopher L.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1353/mon.0.0072">doi:10.1353/mon.0.0072</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ydzwdp5yfjgxjpouwcslzsnaee">fatcat:ydzwdp5yfjgxjpouwcslzsnaee</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_monatshefte-study-of-german-language_winter-2008_100_4/page/560" title="read fulltext microfilm" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_monatshefte-study-of-german-language_winter-2008_100_4/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1353/mon.0.0072"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Personalia 2010

Adam Woodis
<span title="">2010</span> <i title="University of Wisconsin Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mxna42rb7jghdfdybk52dkd3gm" style="color: black;">Monatshefte</a> </i> &nbsp;
P.: Curtis C. Bentzel, Ph.D.* Karen J. Campbell, Ph.D. Jennifer Redmann, Ph.D. Emer.: Peter S. Seadle, Ph.D. BG:1 BM:2 BE:2 BR:2 Furman University Greenville, SC 29613 (L B) Prof.: Jane S.  ...  P.: Lect.: Emert.: Retired: BG:8 Christoph W. Eykman, Ph.D. (lv 1) Michael Resler, Ph.D.*(Iv ID) Monika Totten, Ph.D. (vi) Rachel A. Freudenburg, Ph.D.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1353/mon.2010.0039">doi:10.1353/mon.2010.0039</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l2p476ml25d2bb65nppbjv5xqa">fatcat:l2p476ml25d2bb65nppbjv5xqa</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_monatshefte-study-of-german-language_winter-2010_102_4/page/550" title="read fulltext microfilm" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_monatshefte-study-of-german-language_winter-2010_102_4/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1353/mon.2010.0039"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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