J Chem Inf Model - NAOMI: on the almost trivial task of reading molecules from different file formats.

Tópicos

{ data(1714) softwar(1251) tool(1186) }
{ compound(1573) activ(1297) structur(1058) }
{ take(945) account(800) differ(722) }
{ framework(1458) process(801) describ(734) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ sequenc(1873) structur(1644) protein(1328) }
{ network(2748) neural(1063) input(814) }
{ structur(1116) can(940) graph(676) }
{ control(1307) perform(991) simul(935) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ health(3367) inform(1360) care(1135) }
{ first(2504) two(1366) second(1323) }
{ decis(3086) make(1611) patient(1517) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ studi(2440) review(1878) systemat(933) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ design(1359) user(1324) use(1319) }
{ care(1570) inform(1187) nurs(1089) }
{ system(1050) medic(1026) inform(1018) }
{ perform(1367) use(1326) method(1137) }
{ cost(1906) reduc(1198) effect(832) }
{ use(2086) technolog(871) perceiv(783) }
{ cancer(2502) breast(956) screen(824) }
{ activ(1452) weight(1219) physic(1104) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ model(2220) cell(1177) simul(1124) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

In most cheminformatics workflows, chemical information is stored in files which provide the necessary data for subsequent calculations. The correct interpretation of the file formats is an important prerequisite to obtain meaningful results. Consistent reading of molecules from files, however, is not an easy task. Each file format implicitly represents an underlying chemical model, which has to be taken into consideration when the input data is processed. Additionally, many data sources contain invalid molecules. These have to be identified and either corrected or discarded. We present the chemical file format converter NAOMI, which provides efficient procedures for reliable handling of molecules from the common chemical file formats SDF, MOL2, and SMILES. These procedures are based on a consistent chemical model which has been designed for the appropriate representation of molecules relevant in the context of drug discovery. NAOMI's functionality is tested by round robin file IO exercises with public data sets, which we believe should become a standard test for every cheminformatics tool.

Resumo Limpo

cheminformat workflow chemic inform store file provid necessari data subsequ calcul correct interpret file format import prerequisit obtain meaning result consist read molecul file howev easi task file format implicit repres under chemic model taken consider input data process addit mani data sourc contain invalid molecul identifi either correct discard present chemic file format convert naomi provid effici procedur reliabl handl molecul common chemic file format sdf mol smile procedur base consist chemic model design appropri represent molecul relev context drug discoveri naomi function test round robin file io exercis public data set believ becom standard test everi cheminformat tool

Resumos Similares

J Chem Inf Model - CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids. ( 0,846632595205014 )
J Chem Inf Model - Handling of tautomerism and stereochemistry in compound registration. ( 0,790913527962998 )
J Chem Inf Model - ChemDoodle 6.0. ( 0,780648297702546 )
J Chem Inf Model - ZINC: a free tool to discover chemistry for biology. ( 0,738766959539582 )
J Chem Inf Model - ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 9. Extensible thermodynamic constraints for pure compounds and new model developments. ( 0,728861290800092 )
J Chem Inf Model - hERG me out. ( 0,709790330311994 )
J Med Syst - A data types profile suitable for use with ISO EN 13606. ( 0,693217801797749 )
J Chem Inf Model - Visual characterization and diversity quantification of chemical libraries: 1. creation of delimited reference chemical subspaces. ( 0,691944784211805 )
J Chem Inf Model - ZINClick: a database of 16 million novel, patentable, and readily synthesizable 1,4-disubstituted triazoles. ( 0,691489929176406 )
Comput. Biol. Med. - POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones. ( 0,690217873905225 )
J Chem Inf Model - JGromacs: a Java package for analyzing protein simulations. ( 0,684505769368978 )
J Chem Inf Model - CYANOS: a data management system for natural product drug discovery efforts using cultured microorganisms. ( 0,677300133054762 )
J Chem Inf Model - ChemCalc: a building block for tomorrow's chemical infrastructure. ( 0,669314300587916 )
J Chem Inf Model - AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles. ( 0,658178572302284 )
BMC Med Inform Decis Mak - Clinical software development for the Web: lessons learned from the BOADICEA project. ( 0,655683211921782 )
Comput Methods Programs Biomed - SAS macro programs for geographically weighted generalized linear modeling with spatial point data: applications to health research. ( 0,655098057289559 )
J Med Syst - LAS: a software platform to support oncological data management. ( 0,652484911460882 )
J Chem Inf Model - ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions. ( 0,651699558239999 )
J Chem Inf Model - A general sequence processing and analysis program for protein engineering. ( 0,64394262399757 )
J Chem Inf Model - PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies. ( 0,642348771433128 )
J Chem Inf Model - DockoMatic 2.0: high throughput inverse virtual screening and homology modeling. ( 0,634016321214163 )
J Chem Inf Model - admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. ( 0,630248796193936 )
Brief. Bioinformatics - Architecture for interoperable software in biology. ( 0,629698907056839 )
J Chem Inf Model - Exploring aromatic chemical space with NEAT: novel and electronically equivalent aromatic template. ( 0,627688517045382 )
J Chem Inf Model - Freely available conformer generation methods: how good are they? ( 0,624497937916896 )
J Chem Inf Model - Searching for substructures in fragment spaces. ( 0,61763383765413 )
J Biomed Inform - Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses. ( 0,616613292372619 )
Med Biol Eng Comput - Towards a flexible middleware for context-aware pervasive and wearable systems. ( 0,61530283609852 )
Int J Health Geogr - Open-Source web-based Geographical Information System for health exposure assessment. ( 0,615040796240508 )
J Chem Inf Model - Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps (LiCABEDS) and its application on modeling ligand functionality for 5HT-subtype GPCR families. ( 0,614940046268091 )
Comput Methods Programs Biomed - Raw data extraction from electrocardiograms with Portable Document Format. ( 0,614917965439118 )
J Chem Inf Model - Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches. ( 0,614275887179498 )
Methods Inf Med - MITK diffusion imaging. ( 0,611446476546423 )
Appl Clin Inform - Design and multicentric implementation of a generic software architecture for patient recruitment systems re-using existing HIS tools and routine patient data. ( 0,610360223340706 )
Int J Comput Assist Radiol Surg - The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development. ( 0,609845676657323 )
Int J Comput Assist Radiol Surg - Development and implementation of an integrated mobile situational awareness iPhone application VigiVU? at an academic medical center. ( 0,60684273885043 )
Comput Methods Programs Biomed - An open source tool for heart rate variability spectral analysis. ( 0,606367094261987 )
BMC Med Inform Decis Mak - XML-BSPM: an XML format for storing Body Surface Potential Map recordings. ( 0,605050157868481 )
J Chem Inf Model - Best of both worlds: on the complementarity of ligand-based and structure-based virtual screening. ( 0,60370765581391 )
J Chem Inf Model - Atomdroid: a computational chemistry tool for mobile platforms. ( 0,601216927589313 )
J Biomed Inform - Modular design, application architecture, and usage of a self-service model for enterprise data delivery: the Duke Enterprise Data Unified Content Explorer (DEDUCE). ( 0,6007383978824 )
J Am Med Inform Assoc - Implementation of a deidentified federated data network for population-based cohort discovery. ( 0,600615533442035 )
J Chem Inf Model - Integrated project views: decision support platform for drug discovery project teams. ( 0,599827598588496 )
J Chem Inf Model - Small-molecule 3D structure prediction using open crystallography data. ( 0,599701915376598 )
J Chem Inf Model - Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery. ( 0,59811877223425 )
J Chem Inf Model - Integrated decision support for assessing chemical liabilities. ( 0,597575806489427 )
J Biomed Inform - Mining connections between chemicals, proteins, and diseases extracted from Medline annotations. ( 0,59703836973488 )
Brief. Bioinformatics - Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs. ( 0,596262955002126 )
J Chem Inf Model - Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design. ( 0,594451916538256 )
IEEE Trans Vis Comput Graph - A Survey of Software Frameworks for Cluster-Based Large High-Resolution Displays. ( 0,594102461548566 )
J Chem Inf Model - Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets. ( 0,591978080303189 )
Methods Inf Med - The integration of the risk management process with the lifecycle of medical device software. ( 0,590872720336975 )
J Chem Inf Model - Knowledge-based libraries for predicting the geometric preferences of druglike molecules. ( 0,590316682299467 )
J Chem Inf Model - Identification of novel androgen receptor antagonists using structure- and ligand-based methods. ( 0,590311282194903 )
J Chem Inf Model - ColBioS-FlavRC: a collection of bioselective flavonoids and related compounds filtered from high-throughput screening outcomes. ( 0,589534596770902 )
J Chem Inf Model - TIN-a combinatorial compound collection of synthetically feasible multicomponent synthesis products. ( 0,586050229492613 )
Brief. Bioinformatics - A guide to in silico vaccine discovery for eukaryotic pathogens. ( 0,585712236110372 )
J Chem Inf Model - Managing the computational chemistry big data problem: the ioChem-BD platform. ( 0,584553629908101 )
J Chem Inf Model - Automated recycling of chemistry for virtual screening and library design. ( 0,584356808860062 )
Comput Methods Programs Biomed - AIBench: a rapid application development framework for translational research in biomedicine. ( 0,584148544560264 )
J Chem Inf Model - Identification of multitarget activity ridges in high-dimensional bioactivity spaces. ( 0,582960278492906 )
Methods Inf Med - Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure. ( 0,582730118414556 )
J Chem Inf Model - SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition. ( 0,581183723561682 )
BMC Med Inform Decis Mak - A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience. ( 0,581113108806593 )
J Biomed Inform - The Analytic Information Warehouse (AIW): a platform for analytics using electronic health record data. ( 0,58101660830625 )
Int J Med Inform - A review of ECG storage formats. ( 0,580227214258901 )
Health Informatics J - Implementation of integrated heterogeneous electronic electrocardiography data into Maharaj Nakorn Chiang Mai Hospital Information System. ( 0,580037413353456 )
J Med Syst - Development and evaluation of tools for measuring the quality of experience (QoE) in mHealth applications. ( 0,580037413353456 )
J Chem Inf Model - SAR matrices: automated extraction of information-rich SAR tables from large compound data sets. ( 0,578201162033049 )
J Am Med Inform Assoc - Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets. ( 0,577964641379242 )
J Chem Inf Model - GPU accelerated chemical similarity calculation for compound library comparison. ( 0,577390035713018 )
Methods Inf Med - Supporting translational research on inherited cardiomyopathies through information technology. ( 0,577020953928459 )
AMIA Annu Symp Proc - ARX--A Comprehensive Tool for Anonymizing Biomedical Data. ( 0,576901313961426 )
Int J Med Inform - The Epilepsy Phenome/Genome Project (EPGP) informatics platform. ( 0,576111398228859 )
J Chem Inf Model - Conditional probabilities of activity landscape features for individual compounds. ( 0,575947344364091 )
Methods Inf Med - An epidemiological modeling and data integration framework. ( 0,574865713219439 )
J Chem Inf Model - In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics. ( 0,574762811282066 )
J Chem Inf Model - Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy. ( 0,574674029618121 )
Brief. Bioinformatics - Web scraping technologies in an API world. ( 0,574439028276359 )
Brief. Bioinformatics - A toolbox for developing bioinformatics software. ( 0,573379161051111 )
J Chem Inf Model - Neighborhood-based prediction of novel active compounds from SAR matrices. ( 0,57283798860941 )
Curr Protoc Bioinformatics - Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. ( 0,572311197646763 )
AMIA Annu Symp Proc - The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities. ( 0,572210236475678 )
J Am Med Inform Assoc - iDASH: integrating data for analysis, anonymization, and sharing. ( 0,571695790518447 )
J Chem Inf Model - A multivariate chemical similarity approach to search for drugs of potential environmental concern. ( 0,570336854531661 )
Healthc (Amst) - Supporting HITECH implementation and assessing lessons for the future: The role of program evaluation. ( 0,57030049552987 )
Comput. Biol. Med. - IVUSAngio tool: a publicly available software for fast and accurate 3D reconstruction of coronary arteries. ( 0,570266638029889 )
Comput Biol Chem - Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data. ( 0,570227283257228 )
Comput. Biol. Med. - A robust and extendible framework for medical image registration focused on rapid clinical application deployment. ( 0,569530883626951 )
J Chem Inf Model - Markov logic networks for optical chemical structure recognition. ( 0,567988578964826 )
J Chem Inf Model - Comparative analysis of pharmacophore screening tools. ( 0,567269391997704 )
J Chem Inf Model - Discovery of novel histamine H4 and serotonin transporter ligands using the topological feature tree descriptor. ( 0,567090993201387 )
Comput Methods Programs Biomed - Using off-the-shelf tools for terabyte-scale waveform recording in intensive care: computer system design, database description and lessons learned. ( 0,566915080785651 )
J Integr Bioinform - Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction. ( 0,566784535977018 )
Methods Inf Med - Enabling GeneHunter as a grid service: a case study for implementing analytical services in biomedical grids. ( 0,566519671163434 )
J Biomed Inform - A transparent and transportable methodology for evaluating Data Linkage software. ( 0,562577689111507 )
J Chem Inf Model - Novel mycosin protease MycP1 inhibitors identified by virtual screening and 4D fingerprints. ( 0,562108874289156 )
J Chem Inf Model - Novel method for pharmacophore analysis by examining the joint pharmacophore space. ( 0,561720524586911 )
J Chem Inf Model - Combining horizontal and vertical substructure relationships in scaffold hierarchies for activity prediction. ( 0,56165468676679 )
J Chem Inf Model - Target-independent prediction of drug synergies using only drug lipophilicity. ( 0,56118056356057 )