| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcamd/MorrisGHO96 |
| P356 | DOI | 10.1007/BF00124499 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1007/bf00124499 |
| P698 | PubMed publication ID | 8877701 |
| P50 | author | Garrett M. Morris | Q51386284 |
| P2093 | author name string | D S Goodsell | |
| A J Olson | |||
| R Huey | |||
| P2860 | cites work | Refinement of the influenza virus hemagglutinin by simulated annealing | Q27683720 |
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| High-resolution crystal structure of cytochrome P450cam | Q27728724 | ||
| Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors | Q27731528 | ||
| Satisfying hydrogen bonding potential in proteins | Q27860940 | ||
| pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model | Q29302657 | ||
| Classical electrostatics in biology and chemistry | Q29615082 | ||
| A computational procedure for determining energetically favorable binding sites on biologically important macromolecules | Q30406755 | ||
| A geometric approach to macromolecule-ligand interactions | Q34280176 | ||
| Automated docking of substrates to proteins by simulated annealing | Q34640538 | ||
| Flexible docking and design. | Q40476054 | ||
| A novel nonpeptide HIV-1 protease inhibitor: elucidation of the binding mode and its application in the design of related analogs | Q42283956 | ||
| LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads | Q44114180 | ||
| Automated docking in crystallography: analysis of the substrates of aconitase | Q46055675 | ||
| Prediction of the structure of a receptor-protein complex using a binary docking method | Q46149822 | ||
| Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes. | Q52372459 | ||
| Electrostatic effects in proteins: comparison of dielectric and charge models | Q52422371 | ||
| Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin | Q52423696 | ||
| Automated conformational analysis: algorithms for the efficient construction of low-energy conformations. | Q52473270 | ||
| Calculation of electrostatic potentials in an enzyme active site | Q59067672 | ||
| P433 | issue | 4 | |
| P921 | main subject | automation | Q184199 |
| drug discovery | Q1418791 | ||
| P304 | page(s) | 293-304 | |
| P577 | publication date | 1996-08-01 | |
| P1433 | published in | Journal of Computer - Aided Molecular Design | Q15766522 |
| P1476 | title | Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. | |
| P478 | volume | 10 |
| Q27677636 | (+)-Rutamarin as a Dual Inducer of Both GLUT4 Translocation and Expression Efficiently Ameliorates Glucose Homeostasis in Insulin-Resistant Mice |
| Q40137459 | 3D-QSAR and docking studies of 3-arylquinazolinethione derivatives as selective estrogen receptor modulators. |
| Q56979316 | 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands |
| Q40276857 | 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol |
| Q45027175 | A bifunctional enzyme that has both monoacylglycerol acyltransferase and acyl hydrolase activities |
| Q77832767 | A comparative docking study and the design of potentially selective MMP inhibitors |
| Q52265017 | A comparison of heuristic search algorithms for molecular docking. |
| Q92107770 | A comprehensive review of computational techniques for the prediction of drug side effects |
| Q42557837 | A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking |
| Q33557818 | A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction |
| Q30537961 | A modified HSP70 inhibitor shows broad activity as an anticancer agent |
| Q39302228 | A plausible explanation for enhanced bioavailability of P-gp substrates in presence of piperine: simulation for next generation of P-gp inhibitors. |
| Q34937524 | A review of protein-small molecule docking methods |
| Q24804073 | A role of proton transfer in peroxidase-catalyzed process elucidated by substrates docking calculations |
| Q28251340 | A study on the interaction between 5-Methyluridine and human serum albumin using fluorescence quenching method and molecular modeling |
| Q34197864 | A triad of lys12, lys41, arg78 spatial domain, a novel identified heparin binding site on tat protein, facilitates tat-driven cell adhesion |
| Q27339306 | A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA |
| Q28479059 | AST1306, a novel irreversible inhibitor of the epidermal growth factor receptor 1 and 2, exhibits antitumor activity both in vitro and in vivo |
| Q43515835 | Allosteric inhibition of fructose-1,6-bisphosphatase by anilinoquinazolines |
| Q37894718 | Allosteric inhibition of the hepatitis C virus NS5B polymerase: in silico strategies for drug discovery and development |
| Q38985603 | An ESIPT fluorescent probe sensitive to protein α-helix structures |
| Q43611751 | An improved adaptive genetic algorithm for protein-ligand docking |
| Q55285468 | Andrographolide Inhibits Mechanical and Thermal Hyperalgesia in a Rat Model of HIV-Induced Neuropathic Pain. |
| Q29547658 | AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility |
| Q32079439 | Automated docking and the search for HIV protease inhibitors |
| Q57976077 | Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling |
| Q51555332 | BetaDock: shape-priority docking method based on beta-complex. |
| Q38155468 | Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. |
| Q40029912 | Binding Energy calculation of GSK-3 protein of Human against some anti-diabetic compounds of Momordica charantia linn (Bitter melon). |
| Q57990935 | Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors |
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| Q47442457 | Binding of fullerenes to amyloid beta fibrils: size matters |
| Q42004787 | Binding site and affinity prediction of general anesthetics to protein targets using docking |
| Q31135121 | Binding site characteristics in structure-based virtual screening: evaluation of current docking tools |
| Q58719254 | Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview |
| Q28299479 | C-terminal end and aminoacid Lys48 in HMG-CoA lyase are involved in substrate binding and enzyme activity |
| Q35263970 | CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. |
| Q35181207 | Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study |
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| Q30518005 | Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites |
| Q28281920 | Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening |
| Q39930071 | Characterization of the binding of angiotensin II receptor blockers to human serum albumin using docking and molecular dynamics simulation |
| Q46510509 | Characterization of the interaction between tumor necrosis factor-stimulated gene-6 and heparin: implications for the inhibition of plasmin in extracellular matrix microenvironments. |
| Q28550020 | Cissus quadrangularis Linn. Stem Ethanolic Extract Liberates Reactive Oxygen Species and Induces Mitochondria Mediated Apoptosis in KB Cells |
| Q53501563 | Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. |
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| Q38906597 | Comparative binding mechanism of lupeol compounds with plasma proteins and its pharmacological importance |
| Q38298563 | Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN. |
| Q28534023 | Comparative molecular docking analysis of cytoplasmic dynein light chain DYNLL1 with pilin to explore the molecular mechanism of pathogenesis caused by Pseudomonas aeruginosa PAO |
| Q40534064 | Comparative study of non nucleoside inhibitors with HIV-1 reverse transcriptase based on 3D-QSAR and docking |
| Q33532330 | Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase |
| Q27306357 | Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex |
| Q30366521 | Computational approaches for drug discovery. |
| Q52232508 | Computational coevolution of antiviral drug resistance. |
| Q91787670 | Computational enzymology for degradation of chemical warfare agents: promising technologies for remediation processes |
| Q34127928 | Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge |
| Q37346606 | Computational selection of inhibitors of Abeta aggregation and neuronal toxicity. |
| Q40209013 | Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex |
| Q46703802 | Computational studies and drug design for HIV-1 reverse transcriptase inhibitors of 3',4'-di-O-(S)-camphanoyl-(+)-cis-khellactone (DCK) analogs |
| Q30358238 | Computational studies for the structure and function of mRPE65. |
| Q40817228 | Computational studies of the binding mechanisms of fullerenes to human serum albumin |
| Q45250354 | Computational study on the molecular inclusion of andrographolide by cyclodextrin. |
| Q47889903 | Computer aided drug design and its application to the development of potential drugs for neurodegenerative disorders |
| Q39172414 | Computer aided screening and evaluation of herbal therapeutics against MRSA infections |
| Q34385618 | Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange |
| Q33533343 | Conformational dynamics and ligand binding in the multi-domain protein PDC109 |
| Q77749886 | Conformationally constrained analogues of diacylglycerol (DAG). 15. The indispensable role of the sn-1 and sn-2 carbonyls in the binding of DAG-lactones to protein kinase C (PK-C) |
| Q36558060 | Contrasting binding of fisetin and daidzein in γ-cyclodextrin nanocavity |
| Q33890883 | Covalent modification of Thr302 in cytochrome P450 2B1 by the mechanism-based inactivator 4-tert-butylphenylacetylene |
| Q27668158 | Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis |
| Q27620667 | Crystal structure of trypanosoma cruzi tyrosine aminotransferase: Substrate specificity is influenced by cofactor binding mode |
| Q40189121 | Curcuminoids as inhibitors of thioredoxin reductase: a receptor based pharmacophore study with distance mapping of the active site |
| Q27231136 | DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases |
| Q30770159 | DREAM++: flexible docking program for virtual combinatorial libraries |
| Q39110587 | Defining affinity with the GABAA receptor. |
| Q38779796 | Defining nicotinic agonist binding surfaces through photoaffinity labeling |
| Q28298983 | Definition by functional and structural analysis of two malonyl-CoA sites in carnitine palmitoyltransferase 1A |
| Q38088362 | Design and in silico screening of inhibitors of the cholera toxin |
| Q46335921 | Design and synthesis of bis-amide and hydrazide-containing derivatives of malonic acid as potential HIV-1 integrase inhibitors. |
| Q40547803 | Design and synthesis of novel dihydroxyindole-2-carboxylic acids as HIV-1 integrase inhibitors |
| Q42958736 | Design of novel 4-hydroxy-chromene-2-one derivatives as antimicrobial agents. |
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| Q34451647 | Development of a novel therapy for Lipo-oligosaccharide-induced experimental neuritis: use of peptide glycomimics |
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| Q40503284 | Dietary phytochemicals as potent chemotherapeutic agents against breast cancer: Inhibition of NF-κB pathway via molecular interactions in rel homology domain of its precursor protein p105. |
| Q92097567 | Discovery of anti-SARS coronavirus drug based on molecular docking and database screening |
| Q36882060 | Discovery of protein phosphatase 2C inhibitors by virtual screening |
| Q44450154 | Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase |
| Q33527932 | Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function |
| Q52209897 | Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism. |
| Q52043918 | Docking of small ligands to low-resolution and theoretically predicted receptor structures. |
| Q40744359 | Docking of sulfonamides to carbonic anhydrase II and IV. |
| Q73837352 | Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction |
| Q30495708 | Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets |
| Q37562411 | DockoMatic 2.0: high throughput inverse virtual screening and homology modeling |
| Q54628424 | Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. |
| Q47374327 | Dynamic Docking: A Paradigm Shift in Computational Drug Discovery |
| Q37062254 | EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking |
| Q34257520 | Effects of a commonly occurring genetic polymorphism of human CYP3A4 (I118V) on the metabolism of anandamide. |
| Q38270145 | Efficient docking of peptides to proteins without prior knowledge of the binding site |
| Q45004394 | Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study |
| Q30371845 | Embedded cholesterol in the nicotinic acetylcholine receptor |
| Q41715707 | Engineering microsomal cytochrome P450 2C5 to be a soluble, monomeric enzyme. Mutations that alter aggregation, phospholipid dependence of catalysis, and membrane binding |
| Q44000738 | Engineering the substrate specificity of D-amino-acid oxidase. |
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| Q41583480 | Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method |
| Q33718919 | Evaluating the binding efficiency of pheromone binding protein with its natural ligand using molecular docking and fluorescence analysis |
| Q39317652 | Evaluation and Elucidation Studies of Natural Aglycones for Anticancer Potential using Apoptosis-Related Markers: An In silico Study |
| Q28581845 | Evidence of a new phosphoryl transfer system in nucleotide metabolism |
| Q42656435 | Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods |
| Q45253639 | Exploring inhibitory potential of Curcumin against various cancer targets by in silico virtual screening |
| Q52007298 | Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids. |
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| Q46463779 | Gaba receptor insecticide non-competitive antagonists may bind at allosteric modulator sites |
| Q39344552 | HIV gp120 H375 is unique to HIV-1 subtype CRF01_AE and confers strong resistance to the entry inhibitor BMS-599793, a candidate microbicide drug. |
| Q34174472 | Heparan sulfate biosynthesis: a theoretical study of the initial sulfation step by N-deacetylase/N-sulfotransferase |
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| Q28483632 | Homology modeling of dopamine D2 and D3 receptors: molecular dynamics refinement and docking evaluation |
| Q33826976 | Hsp90/Cdc37 chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A |
| Q37514128 | Human P450s involved in drug metabolism and the use of structural modelling for understanding substrate selectivity and binding affinity |
| Q34624323 | Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design |
| Q52855297 | Identification of Ideal Multi-targeting Bioactive Compounds Against Mur Ligases of Enterobacter aerogenes and Its Binding Mechanism in Comparison with Chemical Inhibitors. |
| Q28507975 | Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity |
| Q36287460 | Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking. |
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| Q34599613 | In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists |
| Q34055749 | In silico docking and electrophysiological characterization of lacosamide binding sites on collapsin response mediator protein-2 identifies a pocket important in modulating sodium channel slow inactivation |
| Q44025568 | In silico exploration of novel phytoligands against probable drug target of Clostridium tetani |
| Q43594206 | In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling |
| Q34573936 | In silico screening for inhibitors of p-glycoprotein that target the nucleotide binding domains |
| Q57239753 | In silico study on the substrate binding manner in human myo-inositol monophosphatase 2 |
| Q51557149 | In vivo antigenotoxic potential and possible mechanism of action of selected 4-hydroxy-2H-chromen-2-one derivatives. |
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| Q33766743 | Inhibition of the NEMO/IKKβ association complex formation, a novel mechanism associated with the NF-κB activation suppression by Withania somnifera's key metabolite withaferin A. |
| Q43990821 | Inhibition of yeast lipase (CRL1) and cholesterol esterase (CRL3) by 6-chloro-2-pyrones: comparison with porcine cholesterol esterase |
| Q46058136 | Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations |
| Q28749567 | Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor |
| Q35004622 | Interactions of the melanocortin-4 receptor with the peptide agonist NDP-MSH. |
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| Q57171026 | Kinetic Characterization of Novel HIV-1 Entry Inhibitors: Discovery of a Relationship between Off-Rate and Potency |
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| Q56797652 | Litchi chinensis-derived terpenoid as anti-HIV-1 protease agent: structural design from molecular dynamics simulations |
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| Q44109231 | Modified AutoDock for accurate docking of protein kinase inhibitors |
| Q37168514 | Modulation of DNA methylation by a sesquiterpene lactone parthenolide |
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| Q54441914 | Molecular dynamic simulations give insight into the mechanism of binding between 2-aminothiazole inhibitors and CDK5. |
| Q53629027 | Molecular dynamic simulations reveal the mechanism of binding between xanthine inhibitors and DPP-4. |
| Q27305203 | Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin |
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| Q40588587 | Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase |
| Q36287824 | Molecular evolution of glutathione S-transferases in the genus Drosophila. |
| Q38722890 | Molecular explorations of substituted 2-(4-phenylquinolin-2-yl) phenols as phosphoinositide 3-kinase inhibitors and anticancer agents |
| Q36370663 | Molecular interaction analysis of cigarette smoke carcinogens NNK and NNAL with enzymes involved in DNA repair pathways: An in silico approach |
| Q36526260 | Molecular interaction studies of HIV-1 matrix protein p17 and heparin: identification of the heparin-binding motif of p17 as a target for the development of multitarget antagonists |
| Q35045705 | Molecular mechanisms of ligand-receptor interactions in transmembrane domain V of the alpha2A-adrenoceptor |
| Q83681461 | Molecular modeling and computational simulation of the photosystem-II reaction center to address isoproturon resistance in Phalaris minor |
| Q44087626 | Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors. |
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| Q38769649 | Monocrotophos Induces the Expression of Xenobiotic Metabolizing Cytochrome P450s (CYP2C8 and CYP3A4) and Neurotoxicity in Human Brain Cells |
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| Q48268478 | N-substituted hydroxynaphthalene imino-oxindole derivatives as new class of PI3-kinase inhibitor and breast cancer drug: Molecular validation and structure-activity relationship studies |
| Q38673283 | NADH oxidase activity of indoleamine 2,3-dioxygenase |
| Q45059758 | NMR structural model of the interaction of herbicides with the photosynthetic reaction center from Rhodobacter sphaeroides |
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| Q48060446 | NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer's disease: an investigation by docking, molecular dynamics, and DFT studies |
| Q33982942 | New class of small nonpeptidyl compounds blocks Plasmodium falciparum development in vitro by inhibiting plasmepsins |
| Q47233654 | New organometallic imines of rhenium(i) as potential ligands of GSK-3β: synthesis, characterization and biological studies |
| Q39584172 | Nitrooxyacyl derivatives of salicylic acid: aspirin-like molecules that covalently inactivate cyclooxygenase-1. |
| Q53241785 | Non-covalent interactions of the carcinogen (+)-anti-BPDE with exon 1 of the human K-ras proto-oncogene. |
| Q35157153 | Novel inhibitor discovery and the conformational analysis of inhibitors of listeriolysin O via protein-ligand modeling. |
| Q33351165 | Novel inhibitors of anthrax edema factor |
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| Q28485154 | Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore |
| Q35650550 | Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism |
| Q28486252 | Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors |
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| Q35835515 | Peptide Triazole Inactivators of HIV-1 Utilize a Conserved Two-Cavity Binding Site at the Junction of the Inner and Outer Domains of Env gp120. |
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| Q37380059 | Polymer-drug interactions in tyrosine-derived triblock copolymer nanospheres: a computational modeling approach |
| Q40325097 | Position and orientation of phalloidin in F-actin determined by X-ray fiber diffraction analysis |
| Q36926994 | Positioning of autoimmune TCR-Ob.2F3 and TCR-Ob.3D1 on the MBP85-99/HLA-DR2 complex |
| Q27675674 | Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis |
| Q28191975 | Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach |
| Q41985042 | Pro-inflammatory secretory phospholipase A2 type IIA binds to integrins alphavbeta3 and alpha4beta1 and induces proliferation of monocytic cells in an integrin-dependent manner |
| Q42173525 | Promising Anti-influenza Properties of Active Constituent of Withania somnifera Ayurvedic Herb in Targeting Neuraminidase of H1N1 Influenza: Computational Study |
| Q39966855 | Protection of retinal cells from ischemia by a novel gap junction inhibitor. |
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| Q30331577 | Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta3 integrin. |
| Q28487707 | Protein-protein docking with F(2)Dock 2.0 and GB-rerank |
| Q41633463 | Quantum mechanics implementation in drug-design workflows: does it really help? |
| Q38774504 | Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664. |
| Q41685096 | Revisiting catalysis by chymotrypsin family serine proteases using peptide substrates and inhibitors with unnatural main chains |
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