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MolVA: Mol* - Towards a common library and tools for web molecular graphics [article]

Alexander Rose, David Sehnal, Jaroslav Koča, Sameer Velankar, Stephen Burley
2018 Figshare  
We present a project called Mol* (/'mol-star/) whose goal is to provide a common library and a set of tools for macromolecular data visualization and analysis.  ...  A common library and a set of tools for working with such macromolecular data sets would streamline this step.  ...  format for macromolecules used at PDBe • PatternQuery -query structural patterns in macromolecules Introducing Mol* • Goal: common library and tools for web molecular graphics and analyses • Collection  ... 
doi:10.6084/m9.figshare.6541262.v1 fatcat:stw5kiksnzeqtogoy2k5nwb7ea

ENBIK2018 - Mol* - Towards a common library and tools for web molecular graphics.pdf [article]

Alexander Rose, David Sehnal, Jaroslav Koča, Sameer Velankar, Stephen Burley
2018 Figshare  
To help streamline this process, we present a project called Mol* (/'mol-star/), a common library and a set of tools for working with macromolecular data sets.  ...  representation, query languages, UI state management, visualization, and tools for efficient data access.  ...  Acknowledgments/Funding Thank you for your attention RCSB PDB is funded by NSF, NIH, DOE https://github.com/molstar/  ... 
doi:10.6084/m9.figshare.6541235 fatcat:igrio2rbgbc2zpxjh77kfrrici

The graphical representation of ADME-related molecule properties for medicinal chemists

Timothy J. Ritchie, Peter Ertl, Richard Lewis
2011 Drug Discovery Today  
The 'bad' library ( Fig. 10b) was prepared several years ago, when it was very common for pharmaceutical companies to generate high molecular weight, lipophilic combinatorial libraries, before the impact  ...  A modified version of the Novartis radar plot above has been implemented at GlaxoSmithKline and is deployed on the web via the Molecular Operating Environment web application environment (http://www.chemcomp.com  ... 
doi:10.1016/j.drudis.2010.11.002 pmid:21074634 fatcat:akzpodbdtjhwpptxx3f4w27uqi

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics

Melanie C Burger
2015 Journal of Cheminformatics  
The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms.  ...  ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary  ...  Acknowledgements MB would like to thank CIHR and the Vesalius Trust for funding Lab 3 D development, and iChemLabs for being available to answer questions during the preparation of the manuscript.  ... 
doi:10.1186/s13321-015-0085-3 pmid:26185528 pmcid:PMC4503857 fatcat:v634zecygja4ffnakxtmqhd3ny

Rubabel: wrapping open Babel with Ruby

Rob Smith, Ryan Williamson, Dan Ventura, John T Prince
2013 Journal of Cheminformatics  
We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.  ...  While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose.  ...  Acknowledgements RS acknowledges the NSF (DGE-0750759) for financial support.  ... 
doi:10.1186/1758-2946-5-35 pmid:23883475 pmcid:PMC3733738 fatcat:77m5iaachbhjxaep3paqaxdzom

Antimalarial Flavonoid-Glycoside from Acacia pennata with Inhibitory Potential Against PfDHFR-TS: An In-silico Study

2021 Biointerface Research in Applied Chemistry  
A compound library of 17 FGs reported to be isolated from A. pennata was prepared and subjected to molecular docking simulation studies.  ...  PyRx 0.8 and AutoDock Vina revealed Pinocembrin-7-O-β-D-glucopyranoside (FG17) as the best PfDHFR-TS inhibitor with a binding affinity of -10.4 kcal/mol and -10.8 kcal/mol, respectively.  ...  Lalthanzara, Department of Zoology, Pachhunga University College, for his valuable technical advice and moral support.  ... 
doi:10.33263/briac124.48714887 fatcat:l6ify5nd5zfl7l7766eqkjlrrq

A bibliometric analysis of the Journal of Molecular Graphics and Modelling

Peter Willett
2007 Journal of Molecular Graphics and Modelling  
The scope of the journal includes all aspects of molecular modelling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and  ...  This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in  ...  Furet, A. Sele, N.C. Cohen, 3D molecular lipophilicity potential profiles -a new tool in molecular modeling, J. Mol.  ... 
doi:10.1016/j.jmgm.2007.03.008 pmid:17434326 fatcat:mkd6pjcwrrgddoead5a4xo57dq

ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex

Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma Chandra
2014 F1000Research  
Jain PC, Varadarajan R: A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal Biochem. 2014; 449: 90-8.  ...  Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry.  ...  Acknowledgements We acknowledge all the members of the NSC lab for useful suggestions during the development of the web-server and visualization of the results.  ... 
doi:10.12688/f1000research.5165.1 pmid:25685322 pmcid:PMC4319546 fatcat:rs4nfm7tgzbz5borueyxw4h3ba

ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex

Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma Chandra
2014 F1000Research  
Jain PC, Varadarajan R: A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal Biochem. 2014; 449: 90-8.  ...  Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry.  ...  Acknowledgements We acknowledge all the members of the NSC lab for useful suggestions during the development of the web-server and visualization of the results.  ... 
doi:10.12688/f1000research.5165.2 pmid:25685322 pmcid:PMC4319546 fatcat:chrxsu6jpzeizilkdzrfw4fi5i

Molecular Docking of Rosmarinic Acid against DNMT1 to Treat Breast Cancer

Debasray Saha
2020 International Journal for Research in Applied Science and Engineering Technology  
The rational drug design together with structure-based modeling and rapid screening tools or potential for the reason that characteristic and developing lead malignant tumor molecules.  ...  Therefore, it is of interest to screen DNMT1 (PDB ID 4WXX) target protein with known ligand compound using computer aided molecular modeling and docking tools.  ...  Molecular docking is a crucial tool in structural biology as well as computer-assisted drug design (CADD).  ... 
doi:10.22214/ijraset.2020.6264 fatcat:kncy4xdlybg57ftuzbndsi7qve

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Sofya I. Scherbinina, Philip V. Toukach
2020 International Journal of Molecular Sciences  
Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.  ...  Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology.  ...  based on a symbol library.  ... 
doi:10.3390/ijms21207702 pmid:33081008 fatcat:sympabhcbzd47k4ll4h2gqiwkq

Exploration of the binding modes of l-asparaginase complexed with its amino acid substrates by molecular docking, dynamics and simulation

Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
2016 3 Biotech  
For the apo state enzyme and ligand bound state complexes molecular dynamics (MD) simulation was performed.  ...  In this present study, homology model of the Erwinaze Ò was developed using MODELLER and the same was validated by various quality indexing tools.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s13205-016-0422-x pmid:28330175 pmcid:PMC4835421 fatcat:irgyt3fqrfbpnp26kod4ygaz7a

Bioinformatic Tools for Identifying Disease Gene and SNP Candidates [chapter]

Sean D. Mooney, Vidhya G. Krishnan, Uday S. Evani
2010 Msphere  
In this protocol manuscript, methods for understanding the molecular functions of single nucleotide polymorphisms (SNPs) and mutations are reviewed and described.  ...  Second, statistical methods have been developed to predict mutations that are likely to have a molecular effect.  ...  The SVM utilized by LS-SNP (32) and the method SNAP (58) are two more recent additions to this library of tools that have web sites available for prediction.  ... 
doi:10.1007/978-1-60327-367-1_17 pmid:20238089 pmcid:PMC3957484 fatcat:z3svbfpslbajrbioo2qrjwwkei

3D Structural Predıctıon Of Catechın Specıfıc Aptamer

Arinaasna MAT TAMİDİ, Nor Azlina AHMAD, Razauden ZULKİFLİ, Huszalina HUSSİN, Muhammad Helmi NADRİ
2021 International journal of life sciences and biotechnology  
It was predicted that these aptamers were the most potential aptamer for catechin recognition tool at laboratory scale based on the docking result.  ...  This paper reports the insilico characterization of single stranded-DNA (ssDNA) aptamers, specific for catechin. 28 primary sequences from DNA-aptamers library screened via systemic evolution of ligands  ...  The most common isomer known is the (+) catechin. Due to its beneficial antioxidant characteristic, it has a wide application in health and medicine.  ... 
doi:10.38001/ijlsb.961138 fatcat:fxadnfku4vaovdvu5lkrejtxd4

CH5M3D: an HTML5 program for creating 3D molecular structures

Clarke W Earley
2013 Journal of Cheminformatics  
Conclusions: A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures.  ...  For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages.  ...  User-defined functions By default, this library provides the necessary tools to allow for viewing and modification of molecular structures.  ... 
doi:10.1186/1758-2946-5-46 pmid:24246004 pmcid:PMC4177146 fatcat:6roacxkp2fgrzha2zaarkuilla
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