The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
Abstract
A novel computational methodology for drug design that accommodates receptor flexibility is described. This "relaxed-complex" method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand-enzyme complexes. This new method serves as the computational analog of the experimental "SAR by NMR" and "tether" methods, which permit a building block approach for constructing a very potent drug.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Bayly, C. I., Cieplak, P., Cornell, W., & Kollman, P. A. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100142a004 · Cited by 8,081
Wang, J., Cieplak, P., & Kollman, P. A. (2000) · Journal of Computational Chemistry · doi:10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-f · Cited by 4,015
Discovering High-Affinity Ligands for Proteins: SAR by NMR
Shuker, S. B., Hajduk, P. J., Meadows, R. P., & Fesik, S. W. (1996) · Science · doi:10.1126/science.274.5292.1531 · Cited by 2,041
Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
Babine, R. E., & Bender, S. L. (1997) · Chemical Reviews · doi:10.1021/cr960370z · Cited by 892
Site-directed ligand discovery
Erlanson, D. A., Braisted, A. C., Raphael, D. R., Randal, M., Stroud, R. M., Gordon, E. M., & Wells, J. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.17.9367 · Cited by 466
Accommodating Protein Flexibility in Computational Drug Design,
Carlson, H. A., & McCammon, J. A. (2000) · Molecular Pharmacology · doi:10.1016/s0026-895x(24)23192-8 · Cited by 324
Self-citationRole of Phosphorylation in Regulation of the Assembly of Endocytic Coat Complexes
Slepnev, V. I., Ochoa, G.-C., Butler, M. H., Grabs, D., & Camilli, P. D. (1998) · Science · doi:10.1126/science.281.5378.821 · Cited by 311
Carlson, B. X., Engblom, A. C., Kristiansen, U., Schousboe, A., & Olsen, R. W. (2000) · Molecular Pharmacology · doi:10.1124/mol.57.3.474 · Cited by 271
Developing a Dynamic Pharmacophore Model for HIV-1 Integrase
Carlson, H. A., Masukawa, K. M., Rubins, K., Bushman, F. D., Jorgensen, W. L., Lins, R. D., Briggs, J. M., & McCammon, J. A. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm990322h · Cited by 259
Self-citationRecent developments in structure-based drug design
Klebe, G. (2000) · Journal of Molecular Medicine · doi:10.1007/s001090000084 · Cited by 256
FKBP12, the 12-kDa FK506-binding protein, is a physiologic regulator of the cell cycle
Aghdasi, B., Ye, K., Resnick, A. C., Huang, A., Ha, H. C., Guo, X., Dawson, T. M., Dawson, V. L., & Snyder, S. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.041614198 · Cited by 147
2-Aryl-2,2-difluoroacetamide FKBP12 Ligands: Synthesis and X-ray Structural Studies
Dubowchik, G. M., Vrudhula, V. M., Dasgupta, B., Ditta, J. L., Chen, T., Sheriff, S., Sipman, K., Witmer, M. R., Tredup, J. A., Vyas, D. M., et al. (2001) · Organic Letters · doi:10.1021/ol0166909 · Cited by 107
Burkhard, P., Taylor, P., & Walkinshaw, M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3411 · Cited by 63
(1998) · doi:10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b
Cited by
Molecular Recognition and Docking Algorithms
Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 788
Combining docking and molecular dynamic simulations in drug design
Alonso, H., Bliznyuk, A. A., & Gready, J. E. (2006) · Medicinal Research Reviews · doi:10.1002/med.20067 · Cited by 759
Huang, S., & Zou, X. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21214 · Cited by 401
A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
Forli, S., & Olson, A. J. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm2005145 · Cited by 290
Leduc, A.-M., Trent, J. O., Wittliff, J. L., Bramlett, K. S., Briggs, S. L., Chirgadze, N. Y., Wang, Y., Burris, T. P., & Spatola, A. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1934759100 · Cited by 222
Metadata
- Authors
- Lin, J.-H., Perryman, A. L., Schames, J. R., & McCammon, J. A.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-04-26
- Volume
- 124
- Issue
- 20
- Pages
- 5632-5633
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2019732485
- Cited by
- 386
- References
- 14
- FWCI
- 12.14
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
