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Novel technologies for virtual screening

Thomas Lengauer, Christian Lemmen, Matthias Rarey, Marc Zimmermann
2004 Drug Discovery Today  
In iterative (or sequential) screening, a medium-sized initial sample of, say, several thousand compounds is proposed for experimental testing.  ...  searching through large chemical databases for molecules that are similar to a given query molecule, representations that allow for a much more time-efficient comparison (or even indexing of the database  ... 
doi:10.1016/s1359-6446(04)02939-3 pmid:14761803 fatcat:kigd5ydnirbphig6cv3ciyp4xy

Solution Structure of Plant Nonspecific Lipid Transfer Protein-2 from Rice (Oryza sativa)

Dharmaraj Samuel, Yaw-Jen Liu, Chao-Sheng Cheng, Ping-Chiang Lyu
2002 Journal of Biological Chemistry  
The C terminus of the protein is very flexible and forms a cap over the hydrophobic cavity.  ...  The three-dimensional structure of rice nonspecific lipid transfer protein (nsLTP2) has been solved for the first time.  ...  Acknowledgments-We acknowledge the Regional Instrument Center, Department of Life Sciences, for NMR experiments. We are grateful to Dr. Corey W. Liu  ... 
doi:10.1074/jbc.m203113200 pmid:12011089 fatcat:6lbheuof3bda7h5mxuuk4zv5iq

A conformational factorisation approach for estimating the binding free energies of macromolecules

Kenji Mochizuki, Chris S. Whittleston, Sandeep Somani, Halim Kusumaatmaja, David J. Wales
2014 Physical Chemistry, Chemical Physics - PCCP  
When varying the size of the rigid region, the free energy difference converges for factorisation of groups at a distance of 14Å from the binding site, which corresponds to 80% of the protein being locally  ...  A further significant gain in efficiency is achieved using a recently developed local rigid body framework in both the sampling and the normal mode analysis, which reduces the number of degrees of freedom  ...  For a fully flexible molecule, κ = 3N − 6 where N is the number of atoms. The number of vibrational modes is reduced if parts of the molecule are rigidified, as described in the next section.  ... 
doi:10.1039/c3cp53537a pmid:24213246 fatcat:ymjrz5worrh2rh4w4z7y3vnc5m

Conformational Sampling of Small Molecules With iCon: Performance Assessment in Comparison With OMEGA

Giulio Poli, Thomas Seidel, Thierry Langer
2018 Frontiers in Chemistry  
Two data sets of high-quality X-ray structures of drug-like small molecules originating from the Protein Data Bank (200 ligands) and the Cambridge Structural Database (481 molecules) were used to validate  ...  Overall, this study proved that iCon is able to generate reliable representative conformational ensembles of drug-like small molecules, yielding results comparable to those showed by OMEGA, and thus is  ...  medium-and small-sized conformer ensembles.  ... 
doi:10.3389/fchem.2018.00229 pmid:29971231 pmcid:PMC6018197 fatcat:6bh2lxsntnf65mpdbylfqgmmvy

3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Victor I. Lesk, Michael J. E. Sternberg
2008 Computer applications in the biosciences : CABIOS  
Flexibility is implemented as a weighted exhaustive conformer search for each clashing pair of molecular branches in a set of 5000 models filtered from around $340 000 initially.  ...  via a server. 3D-Garden (Global And Restrained Docking Exploration Nexus), our benchmarked and server-ready flexible docking system, allows sophisticated programming of surface patches by the user via  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn093 pmid:18326508 fatcat:uprxqqsygfchtnksjxp3omtk2u

The driver design for N2O gas detection system based on tunable interband cascade laser

Lihuan Liao, Jingjing Zhang, Daming Dong, Y. Wang
2019 E3S Web of Conferences  
Considering the influence of power supply stability on the digital-analog hybrid drive circuit of tunable diode laser absorption spectroscopy (TDALS), the high-efficiency TPS5430 is used to design the  ...  to effectively reduce radiation interference to ensure the stability of the drive.  ...  Acknowledgements This work was supported by National key research and development program of China (2016YFD0700202).  ... 
doi:10.1051/e3sconf/20197803002 fatcat:xhhil23oofdwrpuexrpvd5xfwa

Optical data storage in photochromic compounds

William Dallari, Marco Scotto d'Abbusco, Elena Samoylova, Francesca Pignatelli, Athanassia Athanassiou, Roberto Cingolani, Alberto Diaspro, Marco Allione, Robert L. Nelson, François Kajzar, Toshikuni Kaino, Yasuhiro Koike
2011 Organic Photonic Materials and Devices XIII  
Multi-photon processes capability of triggering photochemical reactions and physical changes with micrometer-sized resolution in three dimensions offers a wellsuited means to achieve volumetric storage  ...  Information was recorded within the volume of the media via a multi-photon process achieving high localized photoconversion and the fluorescence emission from the photoconverted molecules when excited  ...  In addition, pulse duration of the IR femtosecond laser broadens when propagating through a dispersive medium, causing a further decrease of the efficiency of the writing process.  ... 
doi:10.1117/12.879839 fatcat:k2z7do5e3ngnjcbu6uudcsbg7i

Critical evaluation of search algorithms for automated molecular docking and database screening

Todd J. A. Ewing, Irwin D. Kuntz
1997 Journal of Computational Chemistry  
By varying the amount of sampling, we can monitor the time convergence of scores and rankings.  ...  We evaluate the performance of each method by screening a small database of molecules to a variety of macromolecular targets.  ...  In our study, a medium-sized molecule is one with 15 to 35 nonhydrogen atoms.  ... 
doi:10.1002/(sici)1096-987x(19970715)18:9<1175::aid-jcc6>3.0.co;2-o fatcat:ecpouhnpinc5hcw2qoqwloeizq

Effects of addition of potassium chloride and ethylene glycol on nanofluidic behaviors

Weiyi Lu, Taewan Kim, Venkata K. Punyamurtula, Aijie Han, Yu Qiao
2011 Journal of Materials Science  
The infiltration pressure can be well described by linear superposition of the contributions of liquid components.  ...  The irreversibility of the liquid motion may be attributed to the unique liquid structures in nanoenvironment.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s10853-011-5334-x fatcat:tu7b4smhzfenffpeob7mvnusta

In Vivo Anti-Leukemia, Quantum Chemical Calculations and ADMET Investigations of Some Quaternary and Isothiouronium Surfactants

Ahmed El-Henawy, Manal Khowdiary, Abdelfattah Badawi, Hussein Soliman
2013 Pharmaceuticals  
The ADMET properties were also studied to gain a clear view of the potential oral bioavailability of these compounds.  ...  Quantum chemical calculations were utilized to explore the electronic structure and stability of these compounds.  ...  From the highest scoring superposition, the limited set of conformers was used in the analysis of molecules with high flexibility capable to achieving complete atom to atom superposition.  ... 
doi:10.3390/ph6050634 pmid:24276171 pmcid:PMC3817726 fatcat:d7onuqv3wjg7hadu6j77nijciu

Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density

Juan Huang, Qin Xu, Zhuo Liu, Nitin Jain, Madhusudan Tyagi, Dong-Qing Wei, Liang Hong
2021 Molecules  
We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus  ...  We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus  ...  The identification of any commercial product or trade name does not imply endorsement or recommendation by the NIST. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules26185693 pmid:34577164 pmcid:PMC8470667 fatcat:b5jheekkfjddtefyjiclh7curu

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

Gaurav Arya, Tamar Schlick
2007 Journal of Chemical Physics  
This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially  ...  We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin ͑oligonucleosome͒  ...  The superposition involves determining the rotation matrix and translation vector that gives the best fit superimposition of the two sets of molecules based on the program PDBSUP created by Rupp and Parkin  ... 
doi:10.1063/1.2428305 pmid:17286462 fatcat:nbl7zgwvkjattexczik43nb44i

A comparison of the Low Mode and Monte Carlo conformational search methods

Carol Parish, Rosina Lombardi, Kent Sinclair, Emelyn Smith, Alla Goldberg, Melissa Rappleye, Myrianne Dure
2002 Journal of Molecular Graphics and Modelling  
is most efficient at searching the space of the larger molecular system.  ...  We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo  ...  Acknowledgements Acknowledgement is made to the Donors of the Petroleum Research Fund, administered by the American Chemical Society, for partial support of this research.  ... 
doi:10.1016/s1093-3263(02)00144-4 pmid:12398344 fatcat:avlbue2fb5gsdaicomfeyjpet4

Nanomolar cationic dendrimeric sulfadiazine as potential antitoxoplasmic agent

M.J. Prieto, D. Bacigalupe, O. Pardini, J.I. Amalvy, C. Venturini, M.J. Morilla, E.L. Romero
2006 International Journal of Pharmaceutics  
Both dendrimers could efficiently load SDZ (SDZ-DG4 and SDZ-DG4.5) up to a ratio of 30 molecules SDZ per dendrimer molecule.  ...  In the search for new strategies that improve the efficacy of treatments with reduced doses of SDZ, we have determined the performance of cationic G4 (DG4) and anionic G4.5 (DG4.5) poly(amidoamine) (PAMAM  ...  Romero are members of the Carrera de Investigador Científico Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina). J.I.  ... 
doi:10.1016/j.ijpharm.2006.05.068 pmid:16920292 fatcat:uhacqcwgbjfjrcmashocy3l7w4

Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach

Glenn Glashagen, Sjoerd Vries, Urszula Uciechowska‐Kaczmarzyk, Sergey A. Samsonov, Samuel Murail, Pierre Tuffery, Martin Zacharias
2019 Proteins: Structure, Function, and Bioinformatics  
Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.  ...  It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions.  ...  C, Superposition of example docking solutions among our top five predictions for target 132 (different color from red to white for the docked CECAM1 molecule, HopQ type II in tan color)  ... 
doi:10.1002/prot.25860 pmid:31785163 fatcat:wldw66tkizeyddbq6wun4ziiai
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