Literature DB >> 29338240

BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.

Sergio Decherchi1,2, Giovanni Bottegoni3, Andrea Spitaleri2,4, Walter Rocchia4, Andrea Cavalli1,5.   

Abstract

In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc molecular dynamics protocols in a novel and task-oriented environment; as a notebook, BiKi (acronym of Binding Kinetics) keeps memory of any activity together with dependencies among them. It offers unique accelerated protein-ligand binding/unbinding methods and other useful tools to gain actionable knowledge from molecular dynamics simulations and to simplify the drug discovery process.

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Year:  2018        PMID： 29338240     DOI： 10.1021/acs.jcim.7b00680

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


  11 in total

1.  Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow.

Authors:  Simone Sciabola; Paolo Benedetti; Giulia D'Arrigo; Rubben Torella; Massimo Baroni; Gabriele Cruciani; Francesca Spyrakis
Journal:  ACS Med Chem Lett       Date:  2018-12-13       Impact factor: 4.345

Review 2.  Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.

Authors:  Sergio Decherchi; Andrea Cavalli
Journal:  Chem Rev       Date:  2020-10-02       Impact factor: 60.622

3.  First-in-class humanized FSH blocking antibody targets bone and fat.

Authors:  Sakshi Gera; Damini Sant; Shozeb Haider; Funda Korkmaz; Tan-Chun Kuo; Mehr Mathew; Helena Perez-Pena; Honglin Xie; Hao Chen; Rogerio Batista; Kejun Ma; Zhen Cheng; Elina Hadelia; Cemre Robinson; Anne Macdonald; Sari Miyashita; Anthony Williams; Gregory Jebian; Hirotaka Miyashita; Anisa Gumerova; Kseniia Ievleva; Pinar Smith; Jiahuan He; Vitaly Ryu; Victoria DeMambro; Matthew A Quinn; Marcia Meseck; Se-Min Kim; T Rajendra Kumar; Jameel Iqbal; Maria I New; Daria Lizneva; Clifford J Rosen; Aaron J Hsueh; Tony Yuen; Mone Zaidi
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-30       Impact factor: 12.779

4.  Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms.

Authors:  Daniel P Duarte; Allan J Lamontanara; Giuseppina La Sala; Sukyo Jeong; Yoo-Kyoung Sohn; Alejandro Panjkovich; Sandrine Georgeon; Tim Kükenshöner; Maria J Marcaida; Florence Pojer; Marco De Vivo; Dmitri Svergun; Hak-Sung Kim; Matteo Dal Peraro; Oliver Hantschel
Journal:  Nat Commun       Date:  2020-05-08       Impact factor: 14.919

5.  Binding kinetics of cariprazine and aripiprazole at the dopamine D3 receptor.

Authors:  Annika Frank; Dóra J Kiss; György M Keserű; Holger Stark
Journal:  Sci Rep       Date:  2018-08-21       Impact factor: 4.379

6.  Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II.

Authors:  Jissy A Kuriappan; Neil Osheroff; Marco De Vivo
Journal:  J Chem Inf Model       Date:  2019-09-09       Impact factor: 4.956

7.  Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight.

Authors:  Eleonora Gianquinto; Ilaria Moscetti; Omar De Bei; Barbara Campanini; Marialaura Marchetti; F Javier Luque; Salvatore Cannistraro; Luca Ronda; Anna Rita Bizzarri; Francesca Spyrakis; Stefano Bettati
Journal:  Sci Rep       Date:  2019-12-09       Impact factor: 4.379

8.  Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking.

Authors:  Nicola Scafuri; Miguel A Soler; Andrea Spitaleri; Walter Rocchia
Journal:  J Chem Theory Comput       Date:  2021-10-15       Impact factor: 6.006

9.  Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.

Authors:  Francesco Di Palma; Sergio Decherchi; Fátima Pardo-Avila; Sauro Succi; Michael Levitt; Gunnar von Heijne; Andrea Cavalli
Journal:  J Chem Theory Comput       Date:  2021-12-09       Impact factor: 6.006

10.  Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.

Authors:  Stefano Motta; Lara Callea; Sara Giani Tagliabue; Laura Bonati
Journal:  Sci Rep       Date:  2018-11-01       Impact factor: 4.379
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