Search Results - "Dahlgren, Markus K"

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space by Lu, Chao, Wu, Chuanjie, Ghoreishi, Delaram, Chen, Wei, Wang, Lingle, Damm, Wolfgang, Ross, Gregory A, Dahlgren, Markus K, Russell, Ellery, Von Bargen, Christopher D, Abel, Robert, Friesner, Richard A, Harder, Edward D

“…We report on the development and validation of the OPLS4 force field. OPLS4 builds upon our previous work with OPLS3e to improve model accuracy on challenging…”
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OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules by Roos, Katarina, Wu, Chuanjie, Damm, Wolfgang, Reboul, Mark, Stevenson, James M, Lu, Chao, Dahlgren, Markus K, Mondal, Sayan, Chen, Wei, Wang, Lingle, Abel, Robert, Friesner, Richard A, Harder, Edward D

“…Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by…”
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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins by Harder, Edward, Damm, Wolfgang, Maple, Jon, Wu, Chuanjie, Reboul, Mark, Xiang, Jin Yu, Wang, Lingle, Lupyan, Dmitry, Dahlgren, Markus K, Knight, Jennifer L, Kaus, Joseph W, Cerutti, David S, Krilov, Goran, Jorgensen, William L, Abel, Robert, Friesner, Richard A

“…The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version…”
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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field by Wang, Lingle, Wu, Yujie, Deng, Yuqing, Kim, Byungchan, Pierce, Levi, Krilov, Goran, Lupyan, Dmitry, Robinson, Shaughnessy, Dahlgren, Markus K, Greenwood, Jeremy, Romero, Donna L, Masse, Craig, Knight, Jennifer L, Steinbrecher, Thomas, Beuming, Thijs, Damm, Wolfgang, Harder, Ed, Sherman, Woody, Brewer, Mark, Wester, Ron, Murcko, Mark, Frye, Leah, Farid, Ramy, Lin, Teng, Mobley, David L, Jorgensen, William L, Berne, Bruce J, Friesner, Richard A, Abel, Robert

“…Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited…”
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Statistical molecular design of a focused salicylidene acylhydrazide library and multivariate QSAR of inhibition of type III secretion in the Gram-negative bacterium Yersinia by Dahlgren, Markus K., Zetterström, Caroline E., Gylfe, Åsa, Linusson, Anna, Elofsson, Mikael

“…A combined application of statistical molecular design (SMD), quantitative structure–activity relationship (QSAR) modeling and prediction of new active…”
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Pre-clinical pharmacokinetics and anti-chlamydial activity of salicylidene acylhydrazide inhibitors of bacterial type III secretion by Ur-Rehman, Tofeeq, Slepenkin, Anatoly, Chu, Hencelyn, Blomgren, Anders, Dahlgren, Markus K, Zetterström, Caroline E, Peterson, Ellena M, Elofsson, Mikael, Gylfe, Åsa

“…Salicylidene acylhydrazides belong to a class of compounds shown to inhibit bacterial type III secretion (T3S) in pathogenic Gram-negative bacteria. This class…”
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Illuminating HIV gp120-Ligand Recognition through Computationally-Driven Optimization of Antibody-Recruiting Molecules by Parker, Christopher G, Dahlgren, Markus K, Tao, Ran N, Li, Don T, Douglass, Jr, Eugene F, Shoda, Takuji, Jawanda, Navneet, Spasov, Krasimir A, Lee, Sangil, Zhou, Nannan, Domaoal, Robert A, Sutton, Richard E, Anderson, Karen S, Jorgensen, William L, Krystal, Mark, Spiegel, David A

“…Here we report on the structure-based optimization of antibody-recruiting molecules targeting HIV gp120 (ARM-H). These studies have leveraged a combination of…”
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Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors by Konze, Kyle D, Bos, Pieter H, Dahlgren, Markus K, Leswing, Karl, Tubert-Brohman, Ivan, Bortolato, Andrea, Robbason, Braxton, Abel, Robert, Bhat, Sathesh

“…The hit-to-lead and lead optimization processes usually involve the design, synthesis, and profiling of thousands of analogs prior to clinical candidate…”
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Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields by Dahlgren, Markus K, Schyman, Patric, Tirado-Rives, Julian, Jorgensen, William L

“…The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10…”
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Synthesis of [4-(2-hydroxyphenyl)thiazol-2-yl]methanones as potential bioisosteres of salicylidene acylhydrazides by Hillgren, J Mikael, Dahlgren, Markus K, To, Tam M, Elofsson, Mikael

“…A focused library of [4-(2-hydroxyphenyl)thiazol-2-yl]methanones was prepared in a four-step synthesis with the aim to obtain potent inhibitors of type III…”
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Synthesis of 2-(2-aminopyrimidine)-2,2-difluoroethanols as potential bioisosters of salicylidene acylhydrazides by Dahlgren, Markus K, Oberg, Christopher T, Wallin, Erika A, Janson, Pär G, Elofsson, Mikael

“…Salicylidene acylhydrazides are inhibitors of type III secretion in several gram-negative pathogens. To further develop the salicylidene acylhydrazides,…”
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Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrödinger Computational Platform by Tang, Haifeng, Jensen, Kristian, Houang, Evelyne, McRobb, Fiona M, Bhat, Sathesh, Svensson, Mats, Bochevarov, Art, Day, Tyler, Dahlgren, Markus K, Bell, Jeffery A, Frye, Leah, Skene, Robert J, Lewis, James H, Osborne, James D, Tierney, Jason P, Gordon, James A, Palomero, Maria A, Gallati, Caroline, Chapman, Robert S L, Jones, Daniel R, Hirst, Kim L, Sephton, Mark, Chauhan, Alka, Sharpe, Andrew, Tardia, Piero, Dechaux, Elsa A, Taylor, Andrea, Waddell, Ross D, Valentine, Andrea, Janssens, Holden B, Aziz, Omar, Bloomfield, Dawn E, Ladha, Sandeep, Fraser, Ian J, Ellard, John M

“…d-Serine is a coagonist of the -methyl d-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, d-serine is synthesized from its…”
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Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor by Dahlgren, Markus K., Baeza Garcia, Alvaro, Hare, Alissa A., Tirado-Rives, Julian, Leng, Lin, Bucala, Richard, Jorgensen, William L.

“…The Plasmodium falciparum orthologue of the human cytokine, macrophage migratory inhibitory factor (PfMIF), is produced by the parasite during malaria…”
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Design, Synthesis, and Multivariate Quantitative Structure−Activity Relationship of SalicylanilidesPotent Inhibitors of Type III Secretion in Yersinia by Dahlgren, Markus K, Kauppi, Anna M, Olsson, Ing-Marie, Linusson, Anna, Elofsson, Mikael

“…Analogues to the salicylanilide N-(4-Chlorophenyl)-2-acetoxy-3,5-diiodobenzamide, 1a, an inhibitor of type III secretion (T3S) in Yersinia, were selected,…”
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Virtual screening reveals allosteric inhibitors of the Toxoplasma gondii thymidylate synthase-dihydrofolate reductase by Sharma, Hitesh, Landau, Mark J, Sullivan, Todd J, Kumar, Vidya P, Dahlgren, Markus K, Jorgensen, William L, Anderson, Karen S

“…The parasite Toxoplasma gondii can lead to toxoplasmosis in those who are immunocompromised. To combat the infection, the enzyme responsible for nucleotide…”
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Discovery of a Novel Class of d‑Amino Acid Oxidase Inhibitors Using the Schrödinger Computational Platform by Tang, Haifeng, Jensen, Kristian, Houang, Evelyne, McRobb, Fiona M., Bhat, Sathesh, Svensson, Mats, Bochevarov, Art, Day, Tyler, Dahlgren, Markus K., Bell, Jeffery A., Frye, Leah, Skene, Robert J., Lewis, James H., Osborne, James D., Tierney, Jason P., Gordon, James A., Palomero, Maria A., Gallati, Caroline, Chapman, Robert S. L., Jones, Daniel R., Hirst, Kim L., Sephton, Mark, Chauhan, Alka, Sharpe, Andrew, Tardia, Piero, Dechaux, Elsa A., Taylor, Andrea, Waddell, Ross D., Valentine, Andrea, Janssens, Holden B., Aziz, Omar, Bloomfield, Dawn E., Ladha, Sandeep, Fraser, Ian J., Ellard, John M.

“…d-Serine is a coagonist of the N-methyl d-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, d-serine is synthesized from its…”
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Illuminating HIV gp120-ligand recognition through computationally-driven optimization of antibody-recruiting moleculesElectronic supplementary information (ESI) available. See DOI: 10.1039/c4sc00484a by Parker, Christopher G, Dahlgren, Markus K, Tao, Ran N, Li, Don T, Douglass, Eugene F, Shoda, Takuji, Jawanda, Navneet, Spasov, Krasimir A, Lee, Sangil, Zhou, Nannan, Domaoal, Robert A, Sutton, Richard E, Anderson, Karen S, Krystal, Mark, Jorgensen, William L, Spiegel, David A

“…Here we report on the structure-based optimization of antibody-recruiting molecules targeting HIV gp120 (ARM-H). These studies have leveraged a combination of…”
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Statistical molecular design of balanced compound libraries for QSAR modeling by Linusson, A, Elofsson, M, Andersson, I E, Dahlgren, M K

“…A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link…”
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Design, Synthesis, and Multivariate Quantitative Structure−Activity Relationship of SalicylanilidesPotent Inhibitors of Type III Secretion in Yersinia by Dahlgren, Markus K., Kauppi, Anna M., Olsson, Ing-Marie, Linusson, Anna, Elofsson, Mikael

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