Filters








2,524 Hits in 5.3 sec

Continuous Molecular Fields Approach Applied to Structure-Activity Modeling [article]

Igor I. Baskin, Nelly I. Zhokhova
2013 arXiv   pre-print
The methodology of the approach is described in this chapter, followed by its application to building regression 3D-QSAR models and conducting virtual screening based on one-class classification models  ...  The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic  ...  Yu.A.Ustynyuk for stimulating discussion and advice. The authors also thank Prof. A.Varnek and Dr. G.Marcou for valuable comments regarding the developed approach.  ... 
arXiv:1311.1495v1 fatcat:wnoyw7t7mzhlfcfa63kv4mrdz4

New Methods For Electronic Structure Calculations on Large Molecules

R A Friesner
1991 Annual review of physical chemistry (Print)  
I also thank many members of the electronic structure community for sharing their insights over the years, some of which appear in this article, with a new arrival to the field. Literature Cited  ...  ACKNOWLEDGMENTS The work in our laboratory described herein has been supported by grants from the National Science Foundation, the National Institutes of Health, and the Department of Energy.  ...  At present, a molecular grid is generated by joining atomic grids composed of spherical shells of points with weights that exactly integrate spherical harmonics up to a certain order (35) , The integration  ... 
doi:10.1146/annurev.pc.42.100191.002013 pmid:1747190 fatcat:xpnxea76lbgs7g3krig52nscxi

New Methods For Electronic Structure Calculations On Large Molecules

R. Friesner
1991 Annual review of physical chemistry (Print)  
I also thank many members of the electronic structure community for sharing their insights over the years, some of which appear in this article, with a new arrival to the field. Literature Cited  ...  ACKNOWLEDGMENTS The work in our laboratory described herein has been supported by grants from the National Science Foundation, the National Institutes of Health, and the Department of Energy.  ...  At present, a molecular grid is generated by joining atomic grids composed of spherical shells of points with weights that exactly integrate spherical harmonics up to a certain order (35) , The integration  ... 
doi:10.1146/annurev.physchem.42.1.341 fatcat:lvimipnlpvczflngn3lskb76ge

wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials

M. Gastegger, L. Schwiedrzik, M. Bittermann, F. Berzsenyi, P. Marquetand
2018 Journal of Chemical Physics  
We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies  ...  The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the undesirable scaling of the latter with increasing number of different elements in a chemical system.  ...  ACKNOWLEDGEMENT We thank Michael Seifner for preliminary work on wACSFs. Allocation of computer time at the Vienna Scientific Cluster (VSC) is gratefully acknowledged.  ... 
doi:10.1063/1.5019667 pmid:29960372 fatcat:acl4forfd5g5fjbcjeokordli4

Modeling Charge Penetration Effects in Water-Water Interactions

Tae Hoon Choi
2014 Bulletin of the Korean Chemical Society (Print)  
This report introduces Gaussian electrostatic models (GEMs) to account for charge penetration effects in water−water interactions, allowing electrostatic interactions to be accurately described.  ...  Three different Gaussian electrostatic models, GEM-3S, GEM-5S, and GEM-6S are designed with s-type Gaussian functions.  ...  The geometry of GEM-5S is adapted from the SAPT-5S model, 18 which is a rigid model based on the vibrational averaged geometry.  ... 
doi:10.5012/bkcs.2014.35.10.2906 fatcat:htasrj7izzakdnw7pjtmca64g4

Progress in developing Poisson-Boltzmann equation solvers

Chuan Li, Lin Li, Marharyta Petukh, Emil Alexov
2013 Molecular Based Mathematical Biology  
to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules.  ...  The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem  ...  Acknowledgments We thank Ray Luo and Guowei Wei for useful discussions and Shannon Stefl for proofreading the manuscript. The work was supported by a grant from NIH, NIGMS, grant number R01GM093937.  ... 
doi:10.2478/mlbmb-2013-0002 pmid:24199185 pmcid:PMC3816640 fatcat:3v7q5ehr3faqpmkcokrgr5lhne

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

Piero Gasparotto, Michele Ceriotti
2014 Journal of Chemical Physics  
Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information.  ...  The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids.  ...  ACKNOWLEDGMENTS The authors would like to thank Gareth Tribello, Federico Giberti and Fabio Pietrucci for a careful reading of the manuscript and useful discussion.  ... 
doi:10.1063/1.4900655 pmid:25381505 fatcat:pw5k3vbaefgzde2ecm5lfcj4cy

Modern Software for Computer Modeling in Quantum Chemistry and Molecular Dynamics

Marina V. Malyshkina, Alexander S. Novikov
2021 Compounds  
The most popular modern programs for quantum chemical and molecular dynamics (classical, ab initio, and QM/MM) calculations, which are relevant for the investigation of nature and various properties of  ...  The base features of HyperChem are presented in the program as a conjunction of 3D visualization and 3D animation with molecular dynamics, molecular mechanics, and quantum calculations on chemical systems  ...  DMol3 [14] is a software package that was developed based on density functional theory (DFT) in conjunction with a numerical radial function basis set.  ... 
doi:10.3390/compounds1030012 fatcat:v2ibexq4gfgivf5oe6kf5bzdza

Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey

Tiago Simões, Daniel Lopes, Sérgio Dias, Francisco Fernandes, João Pereira, Joaquim Jorge, Chandrajit Bajaj, Abel Gomes
2017 Computer graphics forum (Print)  
This survey falls in the scope of molecular graphics and modeling, i.e., a research area at the intersection of computational biology, bioinformatics, computational geometry and computer graphics.  ...  Furthermore, these surveys agree on a simplified classification of cavity detection algorithms into the following classes: sphere-based, grid-based, and Voronoi-based.  ...  geometry and numerical geometry into the field of molecular graphics and modeling.  ... 
doi:10.1111/cgf.13158 pmid:29520122 pmcid:PMC5839519 fatcat:5t4rhndtunhvtmkm32niknst7i

Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models [article]

Tomohide Masuda, Matthew Ragoza, David Ryan Koes
2020 arXiv   pre-print
In this work we describe for the first time a deep generative model that can generate 3D molecular structures conditioned on a three-dimensional (3D) binding pocket.  ...  Deep generative models have been applied with increasing success to the generation of two dimensional molecules as SMILES strings and molecular graphs.  ...  Acknowledgements This work is supported by R01GM108340 from the National Institute of General Medical Sciences, is supported in part by the University of Pittsburgh Center for Research Computing through  ... 
arXiv:2010.14442v3 fatcat:c2yxwp2gcrbdfejpfunvntaaa4

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

László Füsti-Molnár, Kenneth M. Merz
2008 Journal of Chemical Physics  
The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature.  ...  A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities.  ...  ACKNOWLEDGMENTS We thank the NIH ͑GM066859͒ for financial support of this research. One of the authors ͑L.F.M.͒ also thanks Dr. Janos Pinter ͑author of the LGO package͒ for some helpful discussions.  ... 
doi:10.1063/1.2945894 pmid:18624561 pmcid:PMC2669769 fatcat:62rff4cpljbepmkc3r2lgapxbq

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Yu-Hang Tang, Dongkun Zhang, George Em Karniadakis
2018 Journal of Chemical Physics  
Molecular fingerprints, i.e. feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and  ...  In this paper, we present the Density-Encoded Canonically Aligned Fingerprint (DECAF) fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities.  ...  Complete set of orthogonal projection vectors as a canonical coordinate frame In 3D, a complete set of orthogonal bases can be found greedily using the protocol as described in Algorithm 3.  ... 
doi:10.1063/1.5008630 pmid:29352799 fatcat:sjqe2s6u5nbp3dny3q7zec3qke

The GAMESS-UK electronic structure package: algorithms, developments and applications

Martyn F. Guest *, Ian J. Bush, Huub J. J. Van Dam, Paul Sherwood, Jens M. H. Thomas, Joop H. Van Lenthe, Remco W. A. Havenith, John Kendrick
2005 Molecular Physics  
Applications of the code in the areas of enzyme and zeolite catalysis and in spectroscopy are described.  ...  The availability of a wide variety of correlation methods provides the necessary functionality to tackle a number of chemically important tasks, ranging from geometry optimization and transition-state  ...  Acknowledgements The GAMESS-UK program has resulted from the efforts of many researchers: we gratefully acknowledge the collaborative efforts of the following: R.D. Amos  ... 
doi:10.1080/00268970512331340592 fatcat:w4e557pdqbentktbj5e5ftl42u

Machine learning for quantum mechanics in a nutshell

Matthias Rupp
2015 International Journal of Quantum Chemistry  
Models that combine quantum mechanics (QM) with machine learning (ML) promise to deliver the accuracy of QM at the speed of ML.  ...  This hands-on tutorial introduces the reader to QM/ML models based on kernel learning, an elegant, systematically nonlinear form of ML.  ...  Anatole von Lilienfeld for helpful discussions and support via SNF grant PPOOP2 138932. A Dataset The tutorial's dataset is modeled after the one introduced in Ref. 62 .  ... 
doi:10.1002/qua.24954 fatcat:qlaqkula65haxonee7hqupody4

Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer

Lyudmila V. Slipchenko, Mark S. Gordon
2006 Journal of Computational Chemistry  
The performance of two variants of the distributed multipole analysis (DMA) together with two different models for estimating the charge penetration energies was studied using six homonuclear dimers.  ...  Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calculating interaction energies in weakly bonded molecular complexes.  ...  Acknowledgment The authors are very grateful to Professor David Sherrill for providing his SAPT and CCSD(T) data for benzene dimer.  ... 
doi:10.1002/jcc.20520 pmid:17143863 fatcat:s6htvfghvzcsjchwpk3364xrwa
« Previous Showing results 1 — 15 out of 2,524 results