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BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation.
Bryan, Daniel R; Kulp, John L; Mahapatra, Manoj K; Bryan, Richard L; Viswanathan, Usha; Carlisle, Micah N; Kim, Surim; Schutte, William D; Clarke, Kevaughn V; Doan, Tony T; Kulp, John L.
Afiliação
  • Bryan DR; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Kulp JL; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Mahapatra MK; Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States.
  • Bryan RL; Kanak Manjari Institute of Pharmaceutical Sciences, Rourkela 769015, Odisha, India.
  • Viswanathan U; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Carlisle MN; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Kim S; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Schutte WD; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Clarke KV; Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States.
  • Doan TT; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
  • Kulp JL; Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.
J Chem Inf Model ; 63(14): 4229-4236, 2023 07 24.
Article em En | MEDLINE | ID: mdl-37406353
Fragment-based drug design uses data about where, and how strongly, small chemical fragments bind to proteins, to assemble new drug molecules. Over the past decade, we have been successfully using fragment data, derived from thermodynamically rigorous Monte Carlo fragment-protein binding simulations, in dozens of preclinical drug programs. However, this approach has not been available to the broader research community because of the cost and complexity of doing simulations and using design tools. We have developed a web application, called BMaps, to make fragment-based drug design widely available with greatly simplified user interfaces. BMaps provides access to a large repository (>550) of proteins with 100s of precomputed fragment maps, druggable hot spots, and high-quality water maps. Users can also employ their own structures or those from the Protein Data Bank and AlphaFold DB. Multigigabyte data sets are searched to find fragments in bondable orientations, ranked by a binding-free energy metric. The designers use this to select modifications that improve affinity and other properties. BMaps is unique in combining conventional tools such as docking and energy minimization with fragment-based design, in a very easy to use and automated web application. The service is available at https://www.boltzmannmaps.com.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Desenho de Fármacos Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Desenho de Fármacos Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos