Articles - 1ba8 mentioned but not cited (9)
- Benchmarking sets for molecular docking. Huang N, Shoichet BK, Irwin JJ. J Med Chem 49 6789-6801 (2006)
- Molecular docking screens using comparative models of proteins. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. J Chem Inf Model 49 2512-2527 (2009)
- Evaluation of DOCK 6 as a pose generation and database enrichment tool. Brozell SR, Mukherjee S, Balius TE, Roe DR, Case DA, Rizzo RC. J Comput Aided Mol Des 26 749-773 (2012)
- Binding-site assessment by virtual fragment screening. Huang N, Jacobson MP. PLoS One 5 e10109 (2010)
- A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening. Jasper JB, Humbeck L, Brinkjost T, Koch O. J Cheminform 10 15 (2018)
- Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies. Lapillo M, Tuccinardi T, Martinelli A, Macchia M, Giordano A, Poli G. Int J Mol Sci 20 E1023 (2019)
- PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Shin WH, Bures MG, Kihara D. Methods 93 41-50 (2016)
- A molecular evolution algorithm for ligand design in DOCK. Prentis LE, Singleton CD, Bickel JD, Allen WJ, Rizzo RC. J Comput Chem 43 1942-1963 (2022)
- Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking. Li C, Sun J, Palade V. BMC Bioinformatics 21 286 (2020)
Articles citing this publication (26)
- Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function. Reulecke I, Lange G, Albrecht J, Klein R, Rarey M. ChemMedChem 3 885-897 (2008)
- Structure of extracellular tissue factor complexed with factor VIIa inhibited with a BPTI mutant. Zhang E, St Charles R, Tulinsky A. J Mol Biol 285 2089-2104 (1999)
- A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. Patel Y, Gillet VJ, Bravi G, Leach AR. J Comput Aided Mol Des 16 653-681 (2002)
- A potent, proteolysis-resistant inhibitor of kallikrein-related peptidase 6 (KLK6) for cancer therapy, developed by combinatorial engineering. Sananes A, Cohen I, Shahar A, Hockla A, De Vita E, Miller AK, Radisky ES, Papo N. J Biol Chem 293 12663-12680 (2018)
- Active and exo-site inhibition of human factor Xa: structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum. Rios-Steiner JL, Murakami MT, Tulinsky A, Arni RK. J Mol Biol 371 774-786 (2007)
- Investigation of the S3 site of thrombin: design, synthesis and biological activity of 4-substituted 3-amino-2-pyridones incorporating P1-argininals. Reiner JE, Lim-Wilby MS, Brunck TK, Ha-Uong T, Goldman EA, Abelman MA, Nutt RF, Semple JE, Tamura SY. Bioorg Med Chem Lett 9 895-900 (1999)
- Molecular insights into substrate specificity of prostate specific antigen through structural modeling. Singh P, LeBeau AM, Lilja H, Denmeade SR, Isaacs JT. Proteins 77 984-993 (2009)
- Non-covalent thrombin inhibitors featuring P(3)-heterocycles with P(1)-monocyclic arginine surrogates. Reiner JE, Siev DV, Araldi GL, Cui JJ, Ho JZ, Reddy KM, Mamedova L, Vu PH, Lee KS, Minami NK, Gibson TS, Anderson SM, Bradbury AE, Nolan TG, Semple JE. Bioorg Med Chem Lett 12 1203-1208 (2002)
- Novel, potent non-covalent thrombin inhibitors incorporating p(3)-lactam scaffolds. Ho JZ, Gibson TS, Semple JE. Bioorg Med Chem Lett 12 743-748 (2002)
- An oxyanion-hole selective serine protease inhibitor in complex with trypsin. Cui J, Marankan F, Fu W, Crich D, Mesecar A, Johnson ME. Bioorg Med Chem 10 41-46 (2002)
- Asymmetric synthesis of novel quaternary alpha-hydroxy-delta-lactam dipeptide surrogates. Minami NK, Reiner JE, Semple JE. Bioorg Med Chem Lett 9 2625-2628 (1999)
- Non-covalent thrombin inhibitors featuring P3-heterocycles with P1-bicyclic arginine surrogates. Cui JJ, Araldi GL, Reiner JE, Reddy KM, Kemp SJ, Ho JZ, Siev DV, Mamedova L, Gibson TS, Gaudette JA, Minami NK, Anderson SM, Bradbury AE, Nolan TG, Semple JE. Bioorg Med Chem Lett 12 2925-2930 (2002)
- Potent and selective thrombin inhibitors featuring hydrophobic, basic P3-P4-aminoalkyllactam moieties. Semple JE, Rowley DC, Owens TD, Minami NK, Uong TH, Brunck TK. Bioorg Med Chem Lett 8 3525-3530 (1998)
- Alkoxide-catalyzed ring-opening of a novel homosaccharin derivative: synthesis of potent, selective P3-lactam thrombin inhibitors containing P4-o-alkoxycarbonylbenzylsulfonamide residues. Owens TD, Semple JE. Bioorg Med Chem Lett 8 3683-3688 (1998)
- Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials. Hoppe C, Steinbeck C, Wohlfahrt G. J Mol Graph Model 24 328-340 (2006)
- Novel benzo-fused lactam scaffolds as factor Xa inhibitors. Tamura SY, Goldman EA, Bergum PW, Semple JE. Bioorg Med Chem Lett 9 2573-2578 (1999)
- Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure. Hanessian S, Therrien E, van Otterlo WA, Bayrakdarian M, Nilsson I, Fjellström O, Xue Y. Bioorg Med Chem Lett 16 1032-1036 (2006)
- Using peptidyl aldehydes in activity-based proteomics. Sabidó E, Tarragó T, Giralt E. Bioorg Med Chem Lett 19 3752-3755 (2009)
- Crystal structure of highly glycosylated human leukocyte elastase in complex with an S2' site binding inhibitor. Hochscherf J, Pietsch M, Tieu W, Kuan K, Abell AD, Gütschow M, Niefind K. Acta Crystallogr F Struct Biol Commun 74 480-489 (2018)
- Design, synthesis and structure-activity relationship of a series of arginine aldehyde factor Xa inhibitors. Part 1: structures based on the (D)-Arg-Gly-Arg tripeptide sequence. Marlowe CK, Sinha U, Gunn AC, Scarborough RM. Bioorg Med Chem Lett 10 13-16 (2000)
- Protease inhibitors - Part 3. Synthesis of non-basic thrombin inhibitors incorporating pyridinium-sulfanilylguanidine moieties at the P1 site. Scozzafava A, Briganti F, Supuran CT. Eur J Med Chem 34 939-952 (1999)
- Exploratory solid-phase synthesis of factor Xa inhibitors: discovery and application of p3-heterocyclic amides as novel types of non-basic arginine surrogates. Ho JZ, Levy OE, Gibson TS, Nguyen K, Semple JE. Bioorg Med Chem Lett 9 3459-3464 (1999)
- Modeling of factor XIII activation peptide (28-41) V34L mutant bound to thrombin. Nair DG, Sunilkumar PN, Sadasivan C. J Biomol Struct Dyn 26 387-394 (2008)
- Protease inhibitors. Part 2. Weakly basic thrombin inhibitors incorporating sulfonyl-aminoguanidine moieties as S1 anchoring groups: synthesis and structure-activity correlations. Clare BW, Scozzafava A, Briganti F, Iorga B, Supuran CT. J Enzyme Inhib 15 235-264 (2000)
- Protease inhibitors: Part 4. Synthesis of weakly basic thrombin inhibitors incorporating pyridinium-sulfanilylaminoguanidine moieties. Supuran CT, Briganti F, Scozzafava A, Ilies MA. J Enzyme Inhib 15 335-356 (2000)
- Novel inhibitors and activity-based probes targeting serine proteases. Ferguson TEG, Reihill JA, Martin SL, Walker B. Front Chem 10 1006618 (2022)