Derek R. Buckle, Paul Erhardt, C. Robin Ganellin et al. · IUPAC Standards Online · 2016
The evolution that has taken place in medicinal chemistry practice as a result of major advances in genomics and molecular biology arising from the Human Genome Project has carried with it an extensive additional working vocabulary that has become both integrated and essential terminology for the medicinal chemist. Some of this augmented terminology has been adopted from the many related and interlocked scientific disciplines with which the modern medicinal chemist must be conversant, but many other terms have been introduced to define new concepts and ideas as they have arisen. In this supplementary Glossary, we have attempted to collate and define many of the additional terms that are now considered to be essential components of the medicinal chemist’s expanded repertoire.
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2024
Citation: 'cheminformatics' in the IUPAC Compendium of Chemical Terminology, 5th ed.; International Union of Pure and Applied Chemistry; 2025. Online version 5.0.0, 2025. 10.1351/goldbook.11421 • License: The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International for individual terms. Requests for commercial usage of the compendium should be directed to IUPAC.
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Hugo O. Villar · Kirk-Othmer Encyclopedia of Chemical Technology · 2010
Abstract This article provides an introductory overview of some salient aspects of a field that is becoming mission critical to chemical research. As the volume of data generated by all chemistry projects continues to expand, management, analysis, visualization and dissemination of the data has to be automated. Cheminformatics deals with the complex issues that result from this data explosion and the applications that have been generated.
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RWTH Publications (RWTH Aachen)
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Egon Willighagen · Front Matter · 2011
<strong> Update </strong> : the fourth edition <i> </i> is out. Some project are never finished.
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Cornell, Andrew · Figshare · 2019
This repository is mainly to store programs written and used in my thesis project for my Master of Chemistry degree. I will be posting python examples and related items that can be used in the area of cheminformatics.
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Egon Willighagen · Front Matter · 2011
<strong> Update </strong> : the fourth edition <i> </i> is out. Some project are never finished.
Cited by 0Open access
Venkata, Chandrasekhar, Sharma, Nisha, Schaub, Jonas et al. · Zenodo (CERN European Organization for Nuclear Research) · 2025
3.0.2 (2025-02-10) Bug Fixes classyfire tests (1868b38) classyfire tests (6eb3ae1) remove STOUT completely (cb3d8b8)
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Chandrasekhar Venkata, Nisha Sharma, Jonas Schaub et al. · Zenodo (CERN European Organization for Nuclear Research) · 2026
3.8.0 (2026-02-26) Features CDKtoMOl and tests (c17e1ca) Surge 2.0 implementation (61a774c) Surge 2.0 implementation (d40fba9) Bug Fixes bump axios to 1.13.5 to fix CVE DoS vulnerability (a0a8ccd) button activation colour (4c6e076) E203 flake8 (2bbec76) format conversions (aaf0173) package_lock (bbfb016)
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Bender, Andreas · Jagiellonian Digital Library (Jagiellonian University) · 2005
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Venkata, Chandrasekhar, Sharma, Nisha, Schaub, Jonas et al. · Zenodo (CERN European Organization for Nuclear Research) · 2026
3.9.0 (2026-03-17) Features add AnimatedOutlet page transitions with mode=sync overlap (12e6fb2) add breadcrumbs component and wire CommandPalette + Breadcrumbs into App.tsx (c41f6c8) add btn-hover-lift and focus-ring-animate CSS utilities, update Button component (f00ce43) add command palette with navigation registry and shadcn Command component (8d7f333) add ComparisonContext and ComparisonTray components (1f2c174) add ComparisonView, AddToCompareButton, wire into App.tsx (31f26d7) add ESLint v9 flat config, Vitest setup, and smoke test (6a777bc) add feedback component library and error messaging infrastructure (cb80f53) add glass-bold, glass-mobile, clay-interactive, clay-pressed CSS utilities and glass-refraction-hover rule (f2f86d3) add gradient mesh config, bento layout config, useMediaQuery hook, GradientMesh and LiquidGlassFilter components (5efb791) add husky pre-commit hooks and CI workflow (56385f4) add Loader2 spinner to submit buttons across 21 tool views (bf2288e) add shadcn Resizable and ResizableToolPanel wrapper (444b19e) add TypeScript types to services, context, and config (4e5427c) add useDebounce hook and SMILESPreview component with tests (22a93a4) align header width with page content and add ChemAudit to About (5536574) create BentoGrid and BentoCard reusable components (e4575ee) create Vite config, migrate index.html, migrate all env vars (f458af2) enhance molecule cards with hover glow and expand/collapse (7207796) glass treatment for Header and Footer (2d2fe2e) gradient mesh + glass containers on OCSR, About, Privacy, Terms (3a358ed) header fades to transparent on scroll (6c530f5) immersive HomePage with 3D caffeine molecule background (dc2ae43) install React 19, create TypeScript infrastructure, rename all 61 files (57463b2) install shadcn/ui dependencies, configure path aliases, create cn() utility (7c38905) integrate SMILESPreview into SMILESInput component (686c847) manage Ketcher standalone as downloaded dependency (4db70cf) migrate AboutPage buttons and Footer resource cards to shadcn (785f72c) migrate all react-icons and @fortawesome imports to lucide-react (c1f8c7b) migrate ChemPage from sidebar tabs to bento grid (b902c57) migrate ConvertPage, DepictPage, ToolsPage to bento grid layout (a9d0290) migrate framer-motion to motion package with spring physics enhancements (b45c386) migrate OCSRPage and HomePage to shadcn Button and Card (80cfa90) rebuild 3D molecule with bloom postprocessing + neon glow (fc3f525) redesign header as floating glass pill with animated nav (dd5b33d) redesign HomePage with glass hero and bento feature cards (54a340b) refactor 14 chem/ tool views to glass skeletons + error cards (3efcbf9) refactor 7 convert/depict/tools views to glass skeletons + error cards (17e7efc) refine CSS-first Tailwind v4 configuration (55b2c03) remove molecule comparison feature (f9194c4) remove SMILES inline preview feature (ddf41c1) replace alert() with toast.error and delete LoadingScreen (a2ff45e) replace CRA with Vite stack, restructure package.json (04cebd4) replace mobile menu with shadcn/ui Sheet and clean up isDarkMode ternaries (0df92c3) replace native buttons with shadcn/ui Button across all files (9488a48) replace native buttons with shadcn/ui Button across all pages (33f59d4) replace native form inputs with shadcn/ui across all components (ccc2ecc) replace NPlikenessView alert() with glass-bold info expansion box (5ff1015) responsive fixes, navigation wayfinding, scrollbar-hide, and tests (c28cb3d) rewrite CSS to shadcn/ui OKLCH variables, add FOUC prevention, enhance AppContext (63045a6) route-level code splitting with React.lazy and vendor chunk splitting (994bdbe) simplify tab content to 150ms cross-fade, add stagger/layout animations (a759526) unify tab styling with sky/slate palette and ghost variant (66c0044) update Dockerfile and docker-compose for Vite (cf7fcff) upgrade Tailwind CSS v3 to v4 with Vite plugin (cff7d91) upgrade to Node 24, regenerate package-lock.json (623cbf6) wire AddToCompareButton into ChemPage expanded tool cards (a0329de) wire Axios toast interceptor and add feedback component tests (5bec898) wire ResizableToolPanel into BentoCard expanded view (ee39aea) Bug Fixes add husky as root devDependency, remove .planning from tracking (589040b) add Plan 02 dependency to Plan 04 (BentoGrid.tsx) (51ff442) center nav tabs absolutely within header pill (3f5c08d) ci: rename REACT_APP_API_URL to VITE_API_URL in Docker build args (417003c) docker: add all OpenCV system deps for Debian 12 migration (f695abc) docker: switch to openjdk-17 (openjdk-11 unavailable in Debian 12) (fc12195) docker: upgrade base image to fix surge GLIBC_2.34 requirement (764aa6e) docker: use libglib2.0-0 (t64 rename is Debian 13, not 12) (a0fcdd3) docker: use miniconda3:24.11.1-0 (Debian 12, GLIBC 2.36) (8f71b38) feature cards in single row bento grid on wide screens (4cf2bb4) fix blue bar, header cramping, and responsive breakpoints (fa8593a) fix header pill spacing, separator visibility, and layout (e97f6f2) frontend: fix header fade, excess whitespace, and page transition wobble (444d9d3) gitignore (36eecc6) improve header scaling at lg/xl/2xl breakpoints (601cbb6) keep header clickable at all scroll positions, reveal on hover (9215476) minimal 3D molecule with light/dark mode + wider hero card (8c13be1) pill-shaped header, separator, reduced height, day/night toggle (6a83e0a) prevent Ketcher iframe from scroll-jacking parent page (d1cc83e) remove glass-refraction-hover effect per user feedback (28d9c99) remove header top padding to eliminate background bar (d27fbcf) remove unused BentoGrid, bentoLayouts, and ResizableToolPanel (3497d13) resolve all Tailwind v4 migration edge cases (ff1e22c) resolve console errors, animation jank, and header layout issues from UAT (a400b17) restore react-icons and @fortawesome dependencies (77e13f9) revert ChemPage from bento grid to sidebar-tab navigation (65437f4) revert ConvertPage, DepictPage, ToolsPage to tab navigation (4595434) revise plans based on checker feedback (942aef5) revise plans based on checker feedback (1e21def) revise plans based on checker feedback (c725476) revise plans based on checker feedback (27f08cb) switch header to fixed positioning to eliminate color bar (420513f) test: update page transition tests to match new opacity-only animation (ed20373) test: wrap MoleculeCard test in ComparisonProvider (f4728ad) update VISUAL-02 to reflect approved tab-based navigation (efcd5bf) wire AddToCompareButton into ChemPage tab-based results (c47f5b7) Documentation add validation strategy (61801a0) add validation strategy (0084229) add validation strategy (8d50d6c) add validation strategy (88061aa) add validation strategy (8fa9abe) add validation strategy (e7aca94) add validation strategy (373ec4f) add verification report with gap findings (b73c912) capture phase context (c0cd183) capture phase context (74e0bb7) capture phase context (1239447) capture phase context (a46661a) capture phase context (3b95a85) capture phase context (b56ff8a) capture phase context (3423153) complete animation polish plan - page transitions, button interactions, tab cross-fades (d881848) complete BentoGrid + ChemPage migration plan (73030f2) complete bulk component migration plan (51f8c37) complete code splitting and responsive fixes plan (92a3753) complete command palette + breadcrumbs plan (d6d5ad9) complete comparison mode plan (412855e) complete CRA-to-Vite migration plan (c13208b) complete developer tooling plan (6ba59fe) complete Docker update and migration verification plan (019f4bf) complete edge case audit and visual verification plan (93c02d9) complete feedback component library plan (19a9e8d) complete final component pass and visual verification plan (60ee16f) complete foundation plan -- CSS utilities, gradient mesh, bento layouts, components (74a4917) complete frontend modernization research (5231955) complete gap closure plan - NPlikenessView alert + submit button spinners (cc57602) complete gap closure plan -- shadcn Button + Card across all pages (69d8b9e) complete glass sweep and visual polish plan (e86680d) complete icon library consolidation plan (dd7f114) complete inline SMILES preview plan (ef56526) complete motion package migration plan (509f56e) complete page migrations plan (0bbdf9f) complete phase execution (d053292) complete phase execution (b9baf7b) complete phase execution (bc5f022) complete phase execution (5d37ec9) complete phase execution and re-verification (b534d76) complete phase execution and verification (2aaad4b) complete phase execution and verification (6bacc59) complete React 19 + TypeScript strict mode plan (5dc5bb7) complete resizable panels and enhanced molecule cards plan (36cab71) complete shadcn/ui foundation plan (a81db68) complete Tailwind v4 migration plan (696fdfe) complete tool view LoadingScreen refactoring plan (d711464) complete Wave 0 test stubs plan (7abebe4) create gap closure plan for NPlikenessView alert and submit button spinners (b714c76) create gap closure plan for remaining shadcn/ui migrations (5e05004) create phase plan (288aace) create phase plan - animations + power features (319d2cb) create phase plan -- 6 plans across 5 waves (0ccf19d) create phase plan — 3 plans across 2 waves (dd78a54) create phase plan (3 plans, 2 waves) (49c5c49) create phase plan for React 19 + TypeScript 5 + Motion migration (59a1f4e) create phase plan for Tailwind v4 migration (a55d1c0) create roadmap (6 phases) (ac0a21f) define v1 requirements (563f5e1) gap closure research for OCSRPage and HomePage component migration (1a48fed) initialize project (2576e8f) map existing codebase (5157cee) record phase 04.1 context session (d20a6e0) record phase 1 context session (5ea4e72) record phase 2 context session (3ff7dd9) record phase 3 context ses
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Martin, Todd, Williams, Antony · U.S. Environmental Protection Agency · 2024
Presentation to NAMs Training Workshop on April 24-25, 2024 in Durham, NCScience Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
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Chandrasekhar Venkata, Nisha Sharma, Jonas Schaub et al. · Zenodo (CERN European Organization for Nuclear Research) · 2026
3.7.2 (2026-01-13) Bug Fixes Classyfire Test coverage (ed7d058) Classyfire Test coverage (ae7e26a) Classyfire Test coverage (7924a9f) Let FastAPI handle asynchronous tasks (d65c7b9)
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Cornell, Andrew · Figshare · 2019
This repository is mainly to store programs written and used in my thesis project for my Master of Chemistry degree. I will be posting python examples and related items that can be used in the area of cheminformatics.
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Konrad J. Karczewski (107090), Roxana Daneshjou (107092), Russ B. Altman (6158) · Figshare · 2015
<p>New associations discovered by cheminformatics methods. The Similarity Ensemble Approach (SEA) uses ligand similarity methods to discover potential new associations between drugs and targets. Reprinted with permission from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002817#pcbi.1002817-Keiser2" target="_blank">[33]</a>.</p>
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Venkata, Chandrasekhar, Sharma, Nisha, Schaub, Jonas et al. · Zenodo (CERN European Organization for Nuclear Research) · 2024
2.6.1 (2024-11-12) Bug Fixes update CITATION.cff (c972839) update README.md (bd56c3a)
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Stephen Winters‐Hilt, Mark Akeson · DNA and Cell Biology · 2004
A cheminformatics method is described for classification, and biophysical examination, of individual molecules. A novel molecular detector is used--one based on current blockade measurements through a nanometer-scale ion channel (alpha-hemolysin). Classification results are described for blockades caused by DNA molecules in the alpha-hemolysin nanopore detector, with signal analysis and pattern recognition performed using a combination of methods from bioinformatics and machine learning. Due to the size of the alpha-hemolysin protein channel, the blockade events report on one DNA molecule at a time, which enables a variety of reproducible, single-molecule biophysical experiments. To capture the full sensitivity of the nanopore detector's blockade signal, Hidden Markov Models (HMMs) were used with Expectation/Maximization for denoising and for associating a feature vector with the ionic current blockade of each captured DNA molecule. Support Vector Machines (SVMs) that employ novel kernel designs were then used as discriminators. With SVM training performed off-line, and economical HMM processing on-line, blockade classification was possible during capture. HMMs were also used in conjunction with a time-domain finite state automaton (off-line) for feature discovery and kinetics analysis. Analysis of the DNA data indicates a variety of binding (DNA-protein), fraying, and conformational shifts that are consistent with data obtained from thermodynamic analyses (melting curves), X-ray crystallography, and NMR studies. The software tools are designed for analysis of generic blockades in ionic channels, including those in other biological pore-forming toxins, other biological channels in general, and semiconductor-based channels.
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Martin, Todd, Williams, Antony · Figshare · 2024
Presentation to NAMs Training Workshop on April 24-25, 2024 in Durham, NCScience Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
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Richard L. Apodaca · Front Matter · 2007
Names are powerful. For example, if you work in a field that has a well-recognized title, it's easy to talk to non-experts about what you do. Doctors, lawyers, NASCAR drivers, actors, and airline pilots all fall into this category. If, on the other hand, you're a medicinal chemist - well, you've got your work cut out for you. Names are especially important in software design.
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Barbara Zdrazil, Rajarshi Guha · Journal of Cheminformatics · 2022
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