LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
نویسندگان
چکیده
منابع مشابه
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a...
متن کاملOptimization of the OPLS-AA Force Field for Long Hydrocarbons.
The all-atom optimized potentials for liquid simulations (OPLS-AA) force field is a popular force field for simulating biomolecules. However, the current OPLS parameters for hydrocarbons developed using short alkanes cannot reproduce the liquid properties of long alkanes in molecular dynamics simulations. Therefore, the extension of OPLS-AA to (phospho)lipid molecules required for the study of ...
متن کاملWeb-scale Topic Models in Spark: An Asynchronous Parameter Server
In this paper, we train a Latent Dirichlet Allocation (LDA) topic model on the ClueWeb12 data set, a 27-terabyte Web crawl. We extend Spark, a popular tool for performing large-scale data analysis, with an asynchronous parameter server. Such a parameter server provides a distributed and concurrently accessed parameter space for the model. A Metropolis-Hastings based collapsed Gibbs sampler is i...
متن کاملAn automatic test case generator for evaluating implementation of access control policies
One of the main requirements for providing software security is the enforcement of access control policies which aim to protect resources of the system against unauthorized accesses. Any error in the implementation of such policies may lead to undesirable outcomes. For testing the implementation of access control policies, it is preferred to use automated methods which are faster and more relia...
متن کاملProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites
The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites t...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2017
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkx312