News & Events


Sci-Mix at Fall ACS Meeting in Boston

posted Aug 27, 2018, 2:57 PM by Emilio Gallicchio   [ updated Aug 27, 2018, 3:09 PM by Rajat Kumar Pal ]

Rajat Pal explains his recent work on the D3 Dopamine Receptor at the Fall ACS Meeting in Boston. His poster has been selected for the Sci-Mix event. Congratulations!

   

Poster on Analytic Model for Molecular Binding at the Fall ACS Meeting in Boston

posted Aug 27, 2018, 2:48 PM by Emilio Gallicchio

Emilio Gallicchio presented a model to extract physical parameters from alchemical binding free energy profiles at the COMP poster session at the Fall ACS Meeting in Boston.

    https://www.dropbox.com/s/093ozi7101s4jy8/poster_analytic_model.pdf?dl=0

Announcing ICoMPUte!

posted Jun 16, 2018, 2:48 PM by Emilio Gallicchio   [ updated Jun 16, 2018, 3:40 PM ]


The Interdisciplinary Computation & Modeling research Program for Undergraduate students (ICoMPUte) will start in September of 2018. It seeks to promote molecular modeling as a research tool in Chemistry and related fields. The program normally lasts two semesters, during which students work in interdisciplinary teams on projects involving wet lab experiments as well as molecular simulations, computer code development, and chemical physics theory & models.

ICoMPUte is managed by the Department of Chemistry at Brooklyn College. A small stipend is provided to qualified students. The program is supported by a generous grant from the National Science Foundation.

Applications are open for the Fall 2018-Spring 2019 session.

Students in laboratory sciences: Chemistry, Biology, Psychology, and Physics as well as Math, Computer Science and Engineering are encouraged to apply. Students interested in chemistry laboratory work are expected to have completed Organic Chemistry II laboratory. Applications from CUNY students not at Brooklyn College are encouraged.

For further questions and eligibility criteria please contact Prof. Emilio Gallicchio, egallicchio@brooklyn.cuny.edu
    

NSF CAREER Award!

posted May 9, 2018, 9:16 AM by Emilio Gallicchio

 





Very exciting news! The Gallicchio's lab will be supported for the next 5 years by a generous CAREER grant from the National Science Foundation for the project: Theory, Models and Computer Simulation of Molecular Recognition Processes.




These resources will support two graduate students while they investigate novel ways to model the thermodynamics of molecular binding processes. One project is aimed at developing a statistical theory to analyze alchemical binding free energy profiles and extract physical parameters of the molecular complexes, characterizing such things as size, shape, energetic complementarity, flexibility, and polarizability. Automated software tools will be employed to obtain physical parameters for a wide range of molecular complexes and machine learning tools will be used to correlate these to chemical and biological properties. In another project, we will develop techniques to deploy large-scale distributed non-equilibrium simulations of molecular binding onto computational grids. We believe that unlocking the tremendous power of computational grids in this fashion will transform the quality and accessibility of atomistic models of molecular recognition. These advances will be collected and shared with the research community by means of high-quality open-source software tools. The robustness and usefulness of these tools will be continuously assessed by applying them to real-world problems in chemical catalysis and medicinal chemistry faced by our partnering experimental laboratories.

We are also very appreciative of the additional generous support we will receive to run a new and exciting interdisciplinary research program for undergraduate students. Students in this program will receive financial support and resources to spend a whole year to deploy both experimental and computational tools to investigate in depth important chemical and biological systems.

We are determined to make the best possible use these precious resources entrusted to us by the NSF. 

Watch out for more news and information about our activities on this channel. Thanks!


Bruce Berne to give the 33rd Friedman Lecture at Brooklyn College

posted Mar 27, 2018, 11:24 AM by Emilio Gallicchio   [ updated Mar 27, 2018, 11:26 AM ]

Professor Bruce Berne, Columbia University, who graduated from Brooklyn College in 1961, will be honored as the host of the 2018 Friedman Lecture at Brooklyn College on April 19th. The annual Friedman Lecture, organized by the Department of Chemistry, is a long-standing tradition at Brooklyn College. Noble laureates such as Hoffman, Taube, Anfinsen, Corey, and Molina are among past honorees. 

Bruce J. Berne was born in Brooklyn, NY. He received his BS in Chemistry from CUNY Brooklyn College in 1961 and his Ph.D. in Chemical Physics from the University of Chicago in 1964. He is currently the Higgins Professor of Chemistry at Columbia University and a member of the National Academy of Sciences. He is known worldwide as one of the pioneers of computer simulations of molecular systems, which are now an integral part of modern Chemical research and the Chemistry curriculum.

The lecture will be held from 1 pm to 2 pm on April 19th, 2018, in the Tanger Auditorium in the Brooklyn College Library building.

https://drive.google.com/open?id=0B6VXyZtFVHc0U0hSUk1GNktZSzVIc1FLNVVyU3o0ZXdEaWUw


A Step Closer to Reliable Modeling of Protein-Peptide Binding

posted Mar 17, 2018, 9:26 PM by Emilio Gallicchio   [ updated Mar 17, 2018, 9:28 PM ]

Congratulations to Denise Kilburg for her paper in Frontiers Molecular Bioscience: Molecular Recognition:



This work moves the field a bit closer to making alchemical calculations of the absolute binding free energies of protein-peptide complexes a reality. It is not at all easy. The first ingredient is to know when things go wrong. And they do ...

Journal Cover of Organic & Biomolecular Chemistry

posted Jan 4, 2018, 7:46 AM by Emilio Gallicchio

Congratulations to students Danielle Hirsch and Rajat Pal whose paper and artistic rendering of an hydroxytropolone bound to an enzyme of the herpes simplex virus has made the journal cover of Organic & Biomolecular Chemistry

http://dx.doi.org/10.1039/C7OB02453C

Release of the AGBNP1 OpenMM Plugin for GPUs

posted Oct 27, 2017, 11:37 AM by Emilio Gallicchio   [ updated Oct 27, 2017, 11:46 AM ]

The AGBNP (Analytic Generalized Born plus Non-Polar) implicit solvent model is our main solvation force field for alchemical binding free energy calculations. Following the development of the GaussVol algorithm for GPUs, we have just completed the implementation of the AGBNP model version 1 on GPUs as part of the OpenMM library. As we reported earlier, the GPU code is up to 100 times faster than our best CPU implementation. While lacking some of the advanced features of AGBNP2 (solvent-excluded volume representation and hydration sites), this milestone moves us closer to a full port of our alchemical binding free energy software stack to GPU devices. The GPU port of AGBNP2 is underway. 


Support from the National Science Foundation is gratefully acknowledged


Prof. Emilio Gallicchio presents at the Henry Wasser Award ceremony..!!

posted Sep 27, 2017, 7:49 AM by Rajat Kumar Pal   [ updated Oct 23, 2017, 11:29 AM ]

Prof. Emilio Gallicchio, the recipient of the Henry Wasser Award from CUNY will be presenting at the award ceremony at the CUNY Graduate Center, NY on Friday, October 20, 2017..!!
Congratulations!

After the award ceremony on Oct 20, 2017!
In the picture : On the left, Dr. Richard Magliozzo, in the middle, Dr. Emilio Gallicchio and to the right , Dr. Manfred Phillip

NVIDIA Award!

posted Aug 23, 2017, 3:14 PM by Emilio Gallicchio   [ updated Aug 24, 2017, 6:34 AM ]

The Computers in Chemistry Division of the American Chemical Society awarded Prof. Emilio Gallicchio of Brooklyn College the NVIDIA GPU Best Poster Award at the 254th ACS National Meeting & Exposition in Washington DC. Prof. Gallicchio's poster is entitled "Efficient GPU/OpenMM implementation of the AGBNP solvation model for macromolecular binding"

poster

Emilio Gallicchio, egallicchio@brooklyn.cuny.edu, Denise Kilburg, Baofeng Zhang
Brooklyn College, Brooklyn, NY, and Doctoral Programs in Chemistry and Biochemistry, Graduate Center of the City University of New York, New York, NY

The poster describes the GPU implementation of the Analytic Generalized Born plus Non-Polar implicit solvent model (AGBNP) for the OpenMM molecular simulation package. As part of this work, novel recursive computational geometry algorithms have been developed to estimate volumes and surface areas of macromolecules. The Generalized Born pairwise descreening algorithm has been formulated to take advantage of the GPU architecture. The GPU implementation is 50 to 100 times faster than our best CPU implementation. Illustrative applications to binding free energy calculations are presented. OpenMM plugin: github.com/egallicc/openmm_gaussvol_plugin

The generous donation of an impressive Titan Xp GPU by NVIDIA is greatly appreciated. We will put it to good use!
 

1-10 of 50