What's New

June 22, 2018
Our paper describing the new QuanSA approach (Quantitative Surface-Field Analysis) has been published in the Journal of Computer-Aided Molecular Design. The method offers a novel mutliple-instance machine-learning methods for binding affinity and pose prediction. It supplants the QMOD method. It is applicable in cases where ligand structure and activity data are available either with or without a crystallographic structure of the protein target. The method is competitive with the FEP approach when structures are available, and the methods have uncorrelated errors, resulting in improved predictions using the approaches in combination.

March 12, 2017
Our paper reporting an entirely new method for 2D to 3D structure generation and conformational elaboration (called ForceGen) has been published in the Journal of Computer-Aided Molecular Design. The method offers better performance on drug-like molecules than competing methods, and it makes macrocyclic ligands tractable both in terms of speed and results quality.

May 25, 2016
Our new QMOD paper reporting extrapolative affinity and pose prediction has been publised in the Journal of Computer-Aided Molecular Design. The corresponding software, which includes many improvements in both predictive ability and workflow is available within the Surflex software platform v3.066.

May 18, 2015
We have just published a paper on a new cross-docking benchmark (called "PINC [PINC Is Not Cognate]") reporting near-cognate level performance on pose prediction using a knowledge-guided docking protocol that combines ensemble docking, ligand similarity, and protein pocket similarity for ensemble composition choice. The paper is published in the Journal of Computer-Aided Molecular Design.

December 8, 2014
We have just published a paper reporting a surprising case of pharmacological crosstalk between the PPAR-alpha transcription factor and the COX enzymes in the Journal of Computer-Aided Molecular Design.

January 23, 2014
We have published three new papers (see the Publications tab). See the Downloads tab for associated data and software. Additional releases will be made in Q1 2014.

October 1, 2013
We will be presenting recent work on off-target prediction for small molecule therapeutics at the Pacific Symposium on Biocomuting in January.

June 1, 2013
Three students have finished their PhD degrees this year. Please congratulate Dr. Russ Spitzer, Dr. Rocco Varela, and Dr. Emmanuel Yera. They have all moved on to great jobs in the Bay Area.

March 1, 2013
We are pleased to announce that our long-time collaborator, Dr. Ann Cleves, has joined the lab as a Senior Staff Scientist.

October 2, 2012
We are pleased to announce the publication of three new papers. The first is a perspective on computer-aided drug design ("Does your model weigh the same as a duck?" in JCAMD). The second is a detailed docking study that was made as part of special symposium from the Spring 2011 ACS ("Surflex-Dock: Docking benchmarks and the real world" also in JCAMD). The third is an exploration of iterative lead optimization using the Surflex-QMOD method ("Iterative refinement of a binding pocket model: Active computational steering of lead optimization" to appear in J. Med. Chem). See the Publications tab for additional details.

November 17, 2011
We have published two new papers, each reporting novel methods. One generalizes the Surflex-Sim ligand similarity computation to allow for comparison of protein binding sites. The other implements a framework for comparing single molecules to sets of other molecules for off-target prediction using sophisticated surface-based molecular similarity computations. Please visit the Publications tab.

May 1, 2011
We have filled all of our current openings for post-doctoral scholars and for graduate students at this time. We still encourage students to apply to the UCSF PQB Graduate Program, but it is likely that we will not add new students to the lab for some time.

September 15, 2010
We have just published a paper addressing a fundamental limitation of most QSAR methods: their lack of physical meaning. By constructing physical active sites for ligand affinity prediction, not only can our QMOD approach produce accurate predictions of affinity and binding mode, it can do so in cases where structure-activity relationships are highly non-additive (see Publications).

March 9, 2010
Prof. Jain is pleased to deliver the OpenEye CUP XI Annual Levinthal Lecture: Molecular Evolution: The Created and the Creators and the Puzzle of Design.

September 10, 2009
Three new students have joined the lab, all from within the Bioinformatics track of the iPQB program: Russell Spitzer, Rocco Varela, and Emmanuel Yera. We have just published a paper on the induction of physical binding pockets for small molecule activity prediction (see Publications).

April 21, 2009
We have completed moving our laboratories to the UCSF Mission Bay Campus. See the Contact tab above for details. We have just published a paper on small molecule docking that allows for protein pocket adaptation (see Publications). The associated data set has been released (see Downloads).

December 18, 2008
We have released the data from the Pham/Jain 2008 paper on customized scoring functions for docking. Also, we are pleased to point to our latest publication (Langham and Jain, 2008).

April 8, 2008
Dr. Tuan Pham, who completed his PhD in the Jain Lab in December 2007 has accepted a position at a pre-public company in the genomic information space. The company is currently in stealth mode. We wish Tuan the best of luck!

February 5, 2008
We have published two methodological papers in a special issue of the Journal of Computer-Aided Molecular Design that relate to methodological performance testing. An additional paper describing a method for customization of scoring functions has been published separately. See the Publications tab for details.

December 1, 2007
We are pleased to announce three transitions within the laboratory. Dr. Barbara Novak, who received her PhD in the Spring, has joined Agilent Technologies. Dr. Tuan Pham has just completed his dissertation, and he will remain with the laboratory continuing his research in customized scoring functions for molecular docking. Dr. James Langham has joined the lab as a postdoctoral researcher.

March 1, 2007
We are pleased to announce the publication of a major new version of Surflex-Dock in the Journal of Computer-Aided Molecular Design (see the Publications tab). An academic version (with no official support) is available to academic researchers for non-commercial use (please see the Contact tab for an email address). Note that requests for Surflex may take weeks to process, since they are done in batch.

April 7, 2006
We are pleased to announce two transitions from the laboratory. Dr. Chris Kingsley, who received his PhD in the Fall, will be joining the Translational Genomics Institute (TGen) in Phoenix as of May 1, 2006. Dr. Taku Tokuyasu, who has been a post-doctoral scholar in the lab, has taken over as UCSF Comprehensive Cancer Center Informatics Core Manager as of April 1, 2006.

We are also pleased to announce publication of a paper describing a broad application of our molecular similarity approach to a large fraction of the space of known drugs. The paper (Cleves and Jain) will appear in J. Med. Chem. in the first half of 2006.

February 6, 2006
Dr. Lawrence Hon's paper on motif finding in higher organisms (MaMF) has been published in Bioinformatics. Lawrence joined Genentech in late January as a post-doctoral scholar in Dr. Zemin Zhang's laboratory.

January 2, 2006
We are pleased to announce that Lawrence Hon and Chris Kingsley have completed their dissertations and have been awarded PhD degrees from UCSF's Biological and Medical Informatics Graduate Program. Lawrence will be beginning a post-doctoral position at Genentech in January.

November 7, 2005
We are pleased to announce publication of three manuscripts:
1) a paper in J. Med. Chem. on the use of negative data in training scoring functions for molecular docking;
2) a paper in Cancer Informatics presenting a web-based data analysis system called Magellan;
3) a paper in Bioinformatics involving computational pathway recognition called QPACA.
Please see the Publications page.

April 1, 2004
Jane Fridlyand has accepted a position as Assistant Professor with UCSF's Epidemiolgy and Biostatistics Department. She will continue to collaborate with the lab in her new position.