Skip to content

d3-force

Structural basis of PROTAC cooperative recognition for selective protein degradation.The influence of rough lipopolysaccharide structure on molecular interactions with mammalian antimicrobial peptidesNew Synthetic Routes to Triazolo-benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective Bromo and Extra-Terminal (BET) Bromodomain Inhibition.Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions.8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.Discovery of Type II Inhibitors of TGFβ-Activated Kinase 1 (TAK1) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 2 (MAP4K2)SIK2 regulates CRTCs, HDAC4 and glucose uptake in adipocytesMetabotropic Glutamate Receptor 5 Negative Allosteric Modulators: Discovery of 2-Chloro-4-[1-(4-fluorophenyl)-2,5-dimethyl-1H-imidazol-4-ylethynyl]pyridine (Basimglurant, RO4917523), a Promising Novel Medicine for Psychiatric DiseasesNrf2 regulates ROS production by mitochondria and NADPH oxidase.The clinically approved drugs dasatinib and bosutinib induce anti-inflammatory macrophages by inhibiting the salt-inducible kinasesNew Monocyclic, Bicyclic, and Tricyclic Ethynylcyanodienones as Activators of the Keap1/Nrf2/ARE Pathway and Inhibitors of Inducible Nitric Oxide SynthasePalmitoylation of the Na/Ca exchanger cytoplasmic loop controls its inactivation and internalization during stress signalingMolecular Cloning and Functional Characterization of Components of the Capsule Biosynthesis Complex of Neisseria meningitidis Serogroup A TOWARD IN VITRO VACCINE PRODUCTIONA bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probesAn unexpected twist to the activation of IKKβ: TAK1 primes IKKβ for activation by autophosphorylationCrystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognitionThe LKB1-salt-inducible kinase pathway functions as a key gluconeogenic suppressor in the liverCharacterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase3-(2-oxoethylidene)indolin-2-one derivatives activate Nrf2 and inhibit NF-κB: potential candidates for chemoprevention.Carnosic acid stimulates glucose uptake in skeletal muscle cells via a PME-1/PP2A/PKB signalling axisKv1.3 inhibitors have differential effects on glucose uptake and AMPK activity in skeletal muscle cell lines and mouse ex vivo skeletal muscleRestoration of CFTR function in patients with cystic fibrosis carrying the F508del-CFTR mutationParkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65Substrate recognition by the cell surface palmitoyl transferase DHHC5.Dysregulation of ubiquitin homeostasis and β-catenin signaling promote spinal muscular atrophyStructure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar AffinitiesThe Nrf2 regulatory network provides an interface between redox and intermediary metabolismCharacterization of WZ4003 and HTH-01-015 as selective inhibitors of the LKB1-tumour-suppressor-activated NUAK kinasesSynthesis of vitamin D3 analogues with A-ring modifications to directly measure vitamin D levels in biological samplesStructure-activity relationship studies of pyrrolone antimalarial agentsThe Concise Guide to Pharmacology 2013/14.: The Concise Guide to Pharmacology 2013/14: G Protein-Coupled ReceptorsElevated SGK1 predicts resistance of breast cancer cells to Akt inhibitorsMetabolism of inflammation limited by AMPK and pseudo-starvationNrf2 impacts cellular bioenergetics by controlling substrate availability for mitochondrial respirationThe anti-inflammatory compound BAY 11-7082 is a potent inhibitor of Protein Tyrosine PhosphatasesBslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilmInvestigation of acyclic uridine amide and 5′-amido nucleoside analogues as potential inhibitors of the Plasmodium falciparum dUTPaseDiscovery and structure-activity relationships of pyrrolone antimalarialsDe Novo Design of Protein Kinase Inhibitors by in Silico Identification of Hinge Region-Binding FragmentsComprehensive characterization and optimization of anti-LRRK2 (leucine-rich repeat kinase 2) monoclonal antibodiesFrom On-Target to Off-Target Activity: Identification and Optimisation of Trypanosoma brucei GSK3 Inhibitors and Their Characterisation as Anti-Trypanosoma brucei Drug Discovery Lead MoleculesHIF-independent role of prolyl hydroxylases in the cellular response to amino acidsStructural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-onesA novel shogaol analog suppresses cancer cell invasion and inflammation, and displays cytoprotective effects through modulation of NF-κB and Nrf2-Keap1 signaling pathwaysX-ray Crystal Structure of ERK5 (MAPK7) in Complex with a Specific InhibitorThe endosome-lysosome pathway and information generation in the immune system.GSK2578215A; a potent and highly selective 2-arylmethyloxy-5-substitutent-N-arylbenzamide LRRK2 kinase inhibitor.Structure of the TatC core of the twin-arginine protein transport systemThe Ancient Drug Salicylate Directly Activates AMP-Activated Protein KinaseApplication of a novel highly sensitive activity-based probe for detection of cathepsin GAnalysis of the role of Nrf2 in the expression of liver proteins in mice using two-dimensional gel-based proteomicsPINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65Synthesis, Chemical Reactivity as Michael Acceptors, and Biological Potency of Monocyclic Cyanoenones, Novel and Highly Potent Anti-inflammatory and Cytoprotective Agents(1)Design, Synthesis and Biological Evaluation of Trypanosoma brucei Trypanothione Synthetase InhibitorsMitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) as an antiinflammatory target: discovery and in vivo activity of selective pyrazolo[1,5-a]pyrimidine inhibitors using a focused library and structure-based optimization approach.Chemical Proteomic Analysis Reveals the Drugability of the Kinome of Trypanosoma bruceiAvirulence Protein 3a (AVR3a) from the Potato Pathogen Phytophthora infestans Forms Homodimers through Its Predicted Translocation Region and Does Not Specifically Bind PhospholipidsNEDD8 overexpression results in neddylation of ubiquitin substrates by the ubiquitin pathway.Kinome-wide Selectivity Profiling of ATP-competitive Mammalian Target of Rapamycin (mTOR) Inhibitors and Characterization of Their Binding KineticsThe ubiquitin E1 enzyme Ube1 mediates NEDD8 activation under diverse stress conditionsAcinetobacter baumannii FolD ligand complexes – potent inhibitors of folate metabolism and a re‐evaluation of the structure of LY374571Aurora kinase inhibitors: Progress towards the clinicThe AMPK-related kinase SIK2 is regulated by cAMP via phosphorylation at Ser(358) in adipocytesSynergy of Peptide and Sugar in O-GlcNAcase Substrate RecognitionDiscovery of potent and selective covalent inhibitors of JNKPhosphorylation of FOXO3a on Ser-7 by p38 Promotes Its Nuclear Localization in Response to DoxorubicinAMPK: a nutrient and energy sensor that maintains energy homeostasisSynthesis and structure-activity relationships of a novel series of pyrimidines as potent inhibitors of TBK1/IKKε kinases.Peptide inhibitors of the Keap1-Nrf2 protein-protein interactionSmall molecules that bind the Mdm2 RING stabilize and activate p53Reduction in BACE1 decreases body weight, protects against diet-induced obesity and enhances insulin sensitivity in miceAMP-Activated Protein Kinase: A Target for Drugs both Ancient and ModernChanges in the ratio of free NEDD8 to ubiquitin triggers NEDDylation by ubiquitin enzymesFragment-based discovery of 6-substituted isoquinolin-1-amine based ROCK-I inhibitors.A multifunctional protease inhibitor to regulate endolysosomal function.Design, Synthesis, and Structure−Activity Relationship Exploration of 1-Substituted 4-Aroyl-3-hydroxy-5-phenyl-1H-pyrrol-2(5H)-one Analogues as Inhibitors of the Annexin A2−S100A10 Protein Interaction4-benzimidazolyl-3-phenylbutanoic acids as novel PIF-pocket-targeting allosteric inhibitors of protein kinase PKCζ.Optimisation of 6-substituted isoquinolin-1-amine based ROCK-I inhibitorsDesign, Synthesis and Biological Evaluation of Novel Inhibitors of Trypanosoma brucei Pteridine Reductase 1The inhibitory effect of phospholemman on the sodium pump requires its palmitoylation.SCF/β-TrCP promotes glycogen synthase kinase 3-dependent degradation of the Nrf2 transcription factor in a keap1-independent mannerImmunosuppressive but Non-LasR-Inducing Analogues of the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-Oxododecanoyl)-L-homoserine LactoneAbsolute SILAC-Compatible Expression Strain Allows Sumo-2 Copy Number Determination in Clinical SamplesCollateral sensitivity of multidrug-resistant cells to the orphan drug tiopronin.Characterization of a selective inhibitor of the Parkinson's disease kinase LRRK2ATP site-directed inhibitors of protein kinase CK2: an update.Identification of Inhibitors of the Leishmania cdc2-Related Protein Kinase CRK3Polyubiquitin binding to optineurin is required for optimal activation of TANK-binding kinase 1 and production of interferon β.Substrate and Product Analogues as Human O-Glcnac Transferase Inhibitors.The cytoprotective role of the Keap1–Nrf2 pathwayDesign, synthesis and biological evaluation of 6-pyridylmethylaminopurines as CDK inhibitorsAnalgesic omega-Conotoxins CVIE and CVIF Selectively and Voltage-Dependently Block Recombinant and Native N-Type Calcium Channels (vol 77, pg 139, 2010)NF-κB controls energy homeostasis and metabolic adaptation by upregulating mitochondrial respirationDevelopment of 18F-fluorinatable dendrons and their application to cancer cell targetingThe specificities of small molecule inhibitors of the TGFß and BMP pathwaysCatalysis by the nucleolytic ribozymesCharacterization of GSK2334470, a novel and highly specific inhibitor of PDK1N1-Benzyl substituted cambinol analogues as isozyme selective inhibitors of the sirtuin family of protein deacetylasesAMP-activated protein kinase—an energy sensor that regulates all aspects of cell functionOptimisation of the Anti-Trypanosoma brucei Activity of the Opioid Agonist U50488109-294-662-661-65X074-937-457-594-345081-355-367-506-27X048-634-530-447-798137-231-469-269-151031-072-815-607-16X105-312-070-982-098018-515-082-074-296027-228-373-793-594016-712-604-622-721086-316-087-480-933118-309-833-112-117134-672-819-080-83X036-789-224-520-054106-594-488-484-12X125-726-727-125-409161-487-188-181-03X076-538-237-089-675051-324-518-696-462198-017-973-913-570156-653-831-632-101178-739-712-688-618131-486-498-702-07X010-031-167-075-106119-453-428-180-987153-595-914-216-97X148-353-591-913-750019-827-938-996-490184-646-935-269-773186-230-275-872-748165-291-395-706-725047-113-007-956-15X089-019-916-582-397136-000-598-663-919051-072-189-723-758040-766-915-457-886141-482-415-400-338149-129-599-518-595156-286-485-464-499001-353-214-346-040118-479-143-842-720007-641-959-106-118189-040-066-278-226026-244-336-682-442168-286-254-597-740109-916-358-959-05X002-458-268-309-533038-310-729-099-192179-033-965-606-598113-229-447-433-64X077-771-399-719-227183-966-651-664-305013-467-292-050-692079-314-054-163-947110-082-309-221-187128-382-566-327-896143-543-676-408-839005-743-260-244-802026-638-223-054-804048-208-660-423-215159-658-602-048-982077-811-145-153-079170-781-236-728-970144-284-594-583-951139-409-891-293-77X081-017-751-048-013114-963-910-586-828162-513-842-046-362188-803-921-043-695191-147-881-232-285081-817-015-173-962106-530-060-683-82X133-935-409-400-672046-588-899-387-353049-222-171-973-678074-598-665-914-143190-195-697-065-907031-461-589-086-771167-851-091-520-257151-760-923-304-502097-019-537-894-104170-696-774-214-700084-807-525-209-072044-648-704-787-12X150-822-190-827-131051-919-508-851-10X036-251-116-198-69X149-946-446-737-586075-397-286-033-085028-992-308-265-357044-207-676-689-405030-350-713-791-200093-997-239-092-949046-345-437-716-689146-411-731-640-871000-266-572-036-366186-389-876-954-313168-483-508-794-377029-748-240-628-036184-507-509-452-559069-961-069-943-549017-777-392-752-199000-150-893-948-804027-437-502-794-894074-789-039-135-70X063-617-165-524-327019-872-586-012-269103-648-347-913-447007-245-406-573-328008-337-248-044-723197-071-041-313-103098-538-513-984-747019-125-805-246-964172-064-016-145-117007-417-942-335-284005-947-025-410-764116-404-026-640-450090-437-295-781-023197-158-559-918-854076-225-263-850-117049-199-509-181-561179-045-041-176-506004-301-778-674-378111-313-231-732-367092-197-031-561-353192-019-786-423-841076-608-180-638-59X175-263-797-963-040141-694-167-791-759081-203-444-563-604125-348-249-762-351125-850-986-196-787119-397-162-706-860133-023-408-974-285039-847-299-166-952076-641-402-312-988102-485-198-725-150168-829-456-947-639098-813-369-162-741023-180-369-416-862189-473-046-734-005019-633-684-883-828174-501-376-407-235129-062-448-949-030162-916-741-322-002080-026-305-809-343016-698-167-713-829091-325-080-234-401032-206-614-235-635143-271-017-351-983169-312-245-869-778089-818-979-077-305187-517-157-601-239111-583-988-147-450058-026-435-099-506153-651-762-444-327159-766-711-047-610058-933-099-316-100023-452-662-674-373047-432-030-246-04X139-008-712-602-518137-720-748-139-162192-136-893-476-749172-890-893-515-719104-472-615-006-481097-374-332-908-898034-416-075-094-770127-642-274-375-054036-708-909-192-156193-863-590-855-263150-028-859-997-047132-394-716-226-832131-238-819-455-784155-402-461-387-483040-389-070-176-191076-478-479-475-120034-190-802-321-708130-316-719-983-242036-668-261-470-040183-767-289-461-131107-556-164-321-147066-190-726-252-149140-900-012-438-14X058-438-690-312-096004-889-112-130-518193-040-307-473-220188-718-220-131-362087-577-350-425-176191-670-060-004-126041-699-843-843-567180-366-233-781-99X122-739-962-072-793109-274-898-147-341124-179-501-005-870008-694-981-426-172109-611-546-954-080004-378-254-734-355133-997-520-845-569115-381-943-359-61X022-078-711-389-998132-854-391-972-865171-143-110-884-468003-946-199-636-328009-649-401-227-606170-042-571-881-121033-301-273-471-462040-826-560-477-838135-293-472-746-415153-999-081-812-523000-498-778-953-787085-065-777-135-758152-366-692-522-975167-869-142-610-582191-676-336-200-724056-387-403-639-935066-841-401-628-941069-503-782-573-055028-137-796-142-577197-678-301-596-236147-466-934-435-143114-647-123-099-321058-829-130-504-901169-953-034-717-264028-012-588-449-727038-839-140-589-623194-924-906-201-593195-611-964-620-410025-014-524-538-421120-667-268-642-909163-117-320-460-138191-290-593-697-506118-339-847-530-982073-318-370-112-877113-828-920-381-078048-983-957-537-421073-531-962-083-670Fork ↗︎

This module implements a velocity Verlet numerical integrator for simulating physical forces on particles. Force simulations can be used to visualize networks and hierarchies, and to resolve collisions as in bubble charts.

To use this module, create a simulation for an array of nodes and apply the desired forces. Then listen for tick events to render the nodes as they update in your preferred graphics system, such as Canvas or SVG.

See one of: