Journal of Chemical Information and Modeling
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#1Afrah Khairallah (Rhodes University)H-Index: 2
#2Caroline Ross (Rhodes University)H-Index: 4
Last. Özlem Tastan Bishop (Rhodes University)H-Index: 16
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Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP into dihydroneopterin triphosphate (DHNP). DHNP is the first intermediate of the folate de novo biosynthesis pathway in prokaryotic and lower eukaryotic microorganisms and the tetrahydrobiopterin (BH4) biosynthesis pathway in higher eukaryotes. The de novo folate biosynthesis provides essential cofactors for DNA replication, cell division, and synthesis of key amino acids in rapidly replicating pathogen cells, s...
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#1L S R Cavalcante (UC Davis: University of California, Davis)
#2Luke L. Daemen (ORNL: Oak Ridge National Laboratory)H-Index: 20
Last. Adam J. Moule (UC Davis: University of California, Davis)
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We describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the atomic simulation environment (ASE) as an interface, we demonstrate the use of a selection of calculators, including density functional theory (DFT) and density functional tight binding (DFTB), to optimize the structures and calculate interatomic force...
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The large majority of bioactive molecules contain a more or less complex ring system as a central structural element. This central core determines the basic molecule shape, keeps substituents in their proper positions, and often also contributes to the biological activity itself. In this study the ring systems extracted from one billion molecules are processed and differences between rings from bioactive molecules and common synthetic molecules are analyzed. The bioactive rings seem to be distri...
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#1Panagiotis I. Koukos (UU: Utrecht University)H-Index: 6
#2Reau Mf (UU: Utrecht University)
Last. Alexandre M. J. J. Bonvin (UU: Utrecht University)H-Index: 76
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Small-molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small-molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail in a timely and efficient manner. Here, we present a new protocol in HADDOCK (High Ambiguity Driven DOCKing), our integrative modeling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK...
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#1Michael Kilgour (McGill University)H-Index: 7
#2Tao Liu (McGill University)
Last. Lena Simine (McGill University)H-Index: 9
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We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are important to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Existing computational tools used for aptamer design focus on cost-effective secondary structure prediction and motif analysis in the large data sets pro...
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#1Javad Noroozi (UW: University of Waterloo)H-Index: 3
#2William R. Smith (UOIT: University of Ontario Institute of Technology)H-Index: 54
The ability to predict the thermodynamic properties of amine species in CO2-loaded aqueous solutions, including their deprotonation (pKa) and carbamate to bicarbonate reversion (pKc) equilibrium constants and their corresponding standard reaction enthalpies, is of critical importance for the design of improved carbon capture solvents. In this study, we used isocoulombic forms of both reactions to determine these quantities for a large set of aqueous alkanolamine solvent systems. Our hybrid appro...
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#1Lulu Zheng (ECUST: East China University of Science and Technology)H-Index: 2
#2Bin Zhu (ECUST: East China University of Science and Technology)H-Index: 5
Last. Yun Tang (ECUST: East China University of Science and Technology)H-Index: 39
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Two-component crystals such as pharmaceutical cocrystals and salts have been proven as an effective strategy to improve physicochemical and biopharmaceutical properties of drugs. It is not easy to select proper molecular combinations to form two-component crystals. The network-based models have been successfully utilized to guide cocrystal design. Yet, the traditional social network-derived methods based on molecular-interaction topology information cannot directly predict interaction partners f...
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Machine learning is emerging as a new paradigm to rationalize chemical properties for deepening our understanding of chemistry and providing instructive clues on better materials performance. While the complex architecture of machine learning contributes to unprecedented capability in this task, it prevents easy interpretation, leading to extensive criticisms on the lack of physical foundations for the black-box like models. Here, we demonstrate a transfer learning strategy that leverages fundam...
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#1Bahaa Jawad (UMKC: University of Missouri–Kansas City)H-Index: 2
Last. Wai-Yim Ching (UMKC: University of Missouri–Kansas City)H-Index: 77
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The spike protein of SARS-CoV-2 binds to ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation null The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface ...
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#1Brandon Havranek (UIC: University of Illinois at Chicago)H-Index: 1
#2Kui K. Chan (Urbana University)
Last. Shahidul M. Islam (UIC: University of Illinois at Chicago)H-Index: 14
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Even with the availability of vaccines, therapeutic options for COVID-19 still remain highly desirable, especially in hospitalized patients with moderate or severe disease. Soluble ACE2 (sACE2) is a promising therapeutic candidate that neutralizes SARS CoV-2 infection by acting as a decoy. Using computational mutagenesis, we designed a number of sACE2 derivatives carrying three to four mutations. The top-predicted sACE2 decoy based on the in silico mutagenesis scan was subjected to molecular dyn...
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Top fields of study
Virtual screening
Docking (molecular)
Docking (dog)
Quantitative structure–activity relationship
Chemistry
Combinatorial chemistry
Computer science
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