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index.xml
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<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>Ding Group at the Tufts University</title>
<link>https://example.com/</link>
<atom:link href="https://example.com/index.xml" rel="self" type="application/rss+xml" />
<description>Ding Group at the Tufts University</description>
<generator>Wowchemy (https://wowchemy.com)</generator><language>en-us</language><lastBuildDate>Sat, 01 Jun 2030 13:00:00 +0000</lastBuildDate>
<image>
<url>https://example.com/media/icon_hu9244895af7335cf6bfd3349da9d875a5_415013_512x512_fill_lanczos_center_3.png</url>
<title>Ding Group at the Tufts University</title>
<link>https://example.com/</link>
</image>
<item>
<title>Example Event</title>
<link>https://example.com/event/example/</link>
<pubDate>Sat, 01 Jun 2030 13:00:00 +0000</pubDate>
<guid>https://example.com/event/example/</guid>
<description><p>Slides can be added in a few ways:</p>
<ul>
<li><strong>Create</strong> slides using Wowchemy&rsquo;s <a href="https://wowchemy.com/docs/managing-content/#create-slides" target="_blank" rel="noopener"><em>Slides</em></a> feature and link using <code>slides</code> parameter in the front matter of the talk file</li>
<li><strong>Upload</strong> an existing slide deck to <code>static/</code> and link using <code>url_slides</code> parameter in the front matter of the talk file</li>
<li><strong>Embed</strong> your slides (e.g. Google Slides) or presentation video on this page using <a href="https://wowchemy.com/docs/writing-markdown-latex/" target="_blank" rel="noopener">shortcodes</a>.</li>
</ul>
<p>Further event details, including page elements such as image galleries, can be added to the body of this page.</p>
</description>
</item>
<item>
<title>CBayesMBAR is published on J. Chem. Theory Comput.!</title>
<link>https://example.com/post/24-11-23/</link>
<pubDate>Sat, 23 Nov 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-11-23/</guid>
<description><p>Our paper on <a href="https://pubs.acs.org/doi/full/10.1021/acs.jctc.4c00948" target="_blank" rel="noopener">CBayesMBAR</a> is published on JCTC! It provides a principled Bayesian approach to compute free energy differences and uncertainties on perturbation graphs with cycles.</p>
</description>
</item>
<item>
<title>Bayesian Approach for Computing Free Energy on Perturbation Graphs with Cycles</title>
<link>https://example.com/publication/cbayesmbar/</link>
<pubDate>Tue, 19 Nov 2024 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/cbayesmbar/</guid>
<description></description>
</item>
<item>
<title>Welcome to Anjali, Haoming, and John!</title>
<link>https://example.com/post/24-10-18-welcome/</link>
<pubDate>Fri, 18 Oct 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-10-18-welcome/</guid>
<description><p>Our lab is growing! Anjali, Haoming, and John have joined the lab as PhD graduate students. Looking forward to working with you all!</p>
</description>
</item>
<item>
<title>Xinqiang gave a talk on BayesMBAR at the 2024 CHARMM Developer's Meeting in Baltimore.</title>
<link>https://example.com/post/24-07-20/</link>
<pubDate>Sat, 20 Jul 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-07-20/</guid>
<description></description>
</item>
<item>
<title>Introduce coupled BayesMBAR, a principled method for computing free energy on perturbation graphs with cycles!</title>
<link>https://example.com/post/24-07-19-cbayesmbar/</link>
<pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-07-19-cbayesmbar/</guid>
<description><p>Checkout the preprint of the manuscript titled <a href="https://chemrxiv.org/engage/chemrxiv/article-details/669c1a8e01103d79c5b4fa60" target="_blank" rel="noopener">&ldquo;Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles&rdquo;</a></p>
</description>
</item>
<item>
<title>Our paper on using potential contrasting to optimize force fields with experimental data is published on J. Phys. Chem. B.</title>
<link>https://example.com/post/24-07-5/</link>
<pubDate>Sat, 06 Jul 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-07-5/</guid>
<description><p>Checkout the final version <a href="https://pubs.acs.org/doi/full/10.1021/acs.jpcb.4c02147" target="_blank" rel="noopener">&ldquo;Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting&rdquo;</a></p>
</description>
</item>
<item>
<title>Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting</title>
<link>https://example.com/publication/pc_experiments/</link>
<pubDate>Fri, 05 Jul 2024 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/pc_experiments/</guid>
<description></description>
</item>
<item>
<title>Welcome to Kun Yue, John Drohan, and Saki Doi!</title>
<link>https://example.com/post/24-06-15/</link>
<pubDate>Sat, 15 Jun 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-06-15/</guid>
<description><p>Kun joins the lab as the lab&rsquo;s first postdoc. Both John and Saki join the lab as summer interns. Welcome on board!</p>
</description>
</item>
<item>
<title>The second manuscript from the Ding lab is online!</title>
<link>https://example.com/post/24-04-02-pc-experiments/</link>
<pubDate>Tue, 02 Apr 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-04-02-pc-experiments/</guid>
<description><p>Checkout the preprint of the manuscript titled <a href="https://doi.org/10.26434/chemrxiv-2024-lvlwb" target="_blank" rel="noopener">&ldquo;Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting&rdquo;</a></p>
</description>
</item>
<item>
<title>Bayesian Multistate Bennett Acceptance Ratio Methods</title>
<link>https://example.com/publication/bayesmbar/</link>
<pubDate>Thu, 22 Feb 2024 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/bayesmbar/</guid>
<description></description>
</item>
<item>
<title>Our paper on BayesMBAR is published on J. Chem. Theory Comput.</title>
<link>https://example.com/post/24-02-22-bayesmbar/</link>
<pubDate>Thu, 22 Feb 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-02-22-bayesmbar/</guid>
<description><p>Checkout the final version of the paper at <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.3c01212" target="_blank" rel="noopener">&ldquo;Bayesian Multistate Bennett Acceptance Ratio Methods&rdquo;</a></p>
</description>
</item>
<item>
<title>Welcome Ryan Cooley to the group as an undergraduate researcher!</title>
<link>https://example.com/post/24-01-15/</link>
<pubDate>Mon, 15 Jan 2024 00:00:00 +0000</pubDate>
<guid>https://example.com/post/24-01-15/</guid>
<description></description>
</item>
<item>
<title>Welcome to Christine Wong and Sophia Gerogiannis!</title>
<link>https://example.com/post/23-12-27/</link>
<pubDate>Wed, 27 Dec 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/post/23-12-27/</guid>
<description><p>Christine and Sophia will join the group as undergraduate researchers in Spring 2024! Welcome!</p>
</description>
</item>
<item>
<title>Fast Free Energy Estimates from λ-dynamics with Bias-updated Gibbs Sampling</title>
<link>https://example.com/publication/ladybugs/</link>
<pubDate>Thu, 21 Dec 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/ladybugs/</guid>
<description></description>
</item>
<item>
<title>Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks</title>
<link>https://example.com/publication/pc_implicitsolvent/</link>
<pubDate>Thu, 16 Nov 2023 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/pc_implicitsolvent/</guid>
<description></description>
</item>
<item>
<title>Congratulations on the first manuscript from the Ding lab!</title>
<link>https://example.com/post/23-11-4-bayesmbar/</link>
<pubDate>Fri, 03 Nov 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/post/23-11-4-bayesmbar/</guid>
<description><p>Checkout the preprint of the manuscript titled <a href="https://arxiv.org/abs/2310.20699" target="_blank" rel="noopener">&ldquo;Bayesian Multistate Bennett Acceptance Ratio Methods&rdquo;</a></p>
</description>
</item>
<item>
<title>Welcome Khoa to the group!</title>
<link>https://example.com/post/23-10-7/</link>
<pubDate>Sat, 07 Oct 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/post/23-10-7/</guid>
<description><p>Khoa is a freshman at Tufts! He is interested in both chemistry and computer science.</p>
</description>
</item>
<item>
<title>OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates</title>
<link>https://example.com/publication/openabc/</link>
<pubDate>Mon, 11 Sep 2023 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/openabc/</guid>
<description></description>
</item>
<item>
<title>The Ding lab will officially open in the Department of Chemistry at Tufts on August 16th!</title>
<link>https://example.com/post/23-07-16-ding/</link>
<pubDate>Sun, 16 Jul 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/post/23-07-16-ding/</guid>
<description></description>
</item>
<item>
<title>Decorrelating Hi-C Contacts Enhances Identification of the Interactions Driving Genomic Structure and Organization</title>
<link>https://example.com/publication/hic/</link>
<pubDate>Fri, 10 Feb 2023 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/hic/</guid>
<description></description>
</item>
<item>
<title>Computational Drug Design</title>
<link>https://example.com/research_old/project_1/</link>
<pubDate>Sun, 01 Jan 2023 00:00:00 +0000</pubDate>
<guid>https://example.com/research_old/project_1/</guid>
<description><p>Drug discovery is a slow and expensive process. We aim to accelerate drug discovery by developing advanced computational methods. Specifically, we focus on developing efficient and accurate methods for computing protein-ligand binding free energy. Our approaches are based on rigorous synergy between statistical mechanics and machine learning methods. Recent advances in machine learning, especially deep probabilistic models, present great opportunities for developing revolutionary methods for drug design. To learn more about our efforts in this area, please read our recent publications:<a href="https://doi.org/10.1021/acs.jpclett.1c00189">DeepBAR</a> <b>DeepBAR</b></p>
</description>
</item>
<item>
<title>Contrasting Learning of Coarse-Grained Force Fields</title>
<link>https://example.com/publication/potential_contrasting/</link>
<pubDate>Tue, 31 May 2022 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/potential_contrasting/</guid>
<description></description>
</item>
<item>
<title>Coarse-Grained Force Field Development</title>
<link>https://example.com/research_old/project_2/</link>
<pubDate>Sat, 01 Jan 2022 00:00:00 +0000</pubDate>
<guid>https://example.com/research_old/project_2/</guid>
<description></description>
</item>
<item>
<title>Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands</title>
<link>https://example.com/publication/d_gsld/</link>
<pubDate>Sat, 05 Jun 2021 13:16:05 -0500</pubDate>
<guid>https://example.com/publication/d_gsld/</guid>
<description></description>
</item>
<item>
<title>DeepBAR: A Fast and Exact Method for Binding Free Energy Computation</title>
<link>https://example.com/publication/deepbar/</link>
<pubDate>Thu, 25 Feb 2021 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/deepbar/</guid>
<description></description>
</item>
<item>
<title>Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface</title>
<link>https://example.com/publication/tetranucleosome/</link>
<pubDate>Wed, 17 Feb 2021 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/tetranucleosome/</guid>
<description></description>
</item>
<item>
<title>Multiscale Modeling of Biomolecular Condenstates</title>
<link>https://example.com/research_old/project_3/</link>
<pubDate>Fri, 01 Jan 2021 00:00:00 +0000</pubDate>
<guid>https://example.com/research_old/project_3/</guid>
<description><p>More is needed.</p></description>
</item>
<item>
<title>Learning Deep Generative Models with Annealed Importance Sampling</title>
<link>https://example.com/publication/aiwae/</link>
<pubDate>Fri, 11 Dec 2020 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/aiwae/</guid>
<description></description>
</item>
<item>
<title>Computing Absolute Free Energy with Deep Generative Models</title>
<link>https://example.com/publication/dgm_bar/</link>
<pubDate>Tue, 03 Nov 2020 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/dgm_bar/</guid>
<description></description>
</item>
<item>
<title>Accelerated CDOCKER with GPUs, parallel simulated annealing and fast Fourier transforms</title>
<link>https://example.com/publication/fft_cdocker/</link>
<pubDate>Fri, 01 May 2020 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/fft_cdocker/</guid>
<description></description>
</item>
<item>
<title>Method Development Combining MD and ML</title>
<link>https://example.com/research_old/project_4/</link>
<pubDate>Wed, 01 Jan 2020 00:00:00 +0000</pubDate>
<guid>https://example.com/research_old/project_4/</guid>
<description><p>When new problems and challenges arise and existing methods fall short,
we develop</p>
</description>
</item>
<item>
<title>Deciphering Protein Evolution and Fitness Landscapes with Latent Space Models</title>
<link>https://example.com/publication/pevae/</link>
<pubDate>Mon, 28 Oct 2019 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/pevae/</guid>
<description></description>
</item>
<item>
<title>Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations</title>
<link>https://example.com/publication/fastmbar/</link>
<pubDate>Mon, 28 Jan 2019 13:08:25 -0500</pubDate>
<guid>https://example.com/publication/fastmbar/</guid>
<description></description>
</item>
<item>
<title>CDOCKER and λ-dynamics for Prospective Prediction in D3R Grand Challenge 2</title>
<link>https://example.com/publication/d3r/</link>
<pubDate>Mon, 01 Jan 2018 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/d3r/</guid>
<description></description>
</item>
<item>
<title>Gibbs Sampler-based λ-dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation</title>
<link>https://example.com/publication/gsld/</link>
<pubDate>Fri, 26 May 2017 13:16:05 -0500</pubDate>
<guid>https://example.com/publication/gsld/</guid>
<description></description>
</item>
<item>
<title>Mechanism of Vps4 Hexamer Function Revealed by Cryo-EM</title>
<link>https://example.com/publication/vps4/</link>
<pubDate>Sat, 01 Apr 2017 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/vps4/</guid>
<description></description>
</item>
<item>
<title>Improved Prediction of RNA Secondary Structure by Integrating the Free Energy Model with Restraints Derived from Experimental Probing Data</title>
<link>https://example.com/publication/rna-lulab/</link>
<pubDate>Mon, 13 Jul 2015 00:00:00 +0000</pubDate>
<guid>https://example.com/publication/rna-lulab/</guid>
<description></description>
</item>
<item>
<title></title>
<link>https://example.com/admin/config.yml</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/admin/config.yml</guid>
<description></description>
</item>
<item>
<title></title>
<link>https://example.com/contact/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/contact/</guid>
<description></description>
</item>
<item>
<title></title>
<link>https://example.com/people/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/people/</guid>
<description></description>
</item>
<item>
<title>BayesMBAR</title>
<link>https://example.com/software/bayesmbar/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/software/bayesmbar/</guid>
<description></description>
</item>
<item>
<title>FastMBAR</title>
<link>https://example.com/software/fastmbar/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/software/fastmbar/</guid>
<description></description>
</item>
<item>
<title>Potential Contrasting</title>
<link>https://example.com/software/pc/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/software/pc/</guid>
<description></description>
</item>
<item>
<title>Research Interest</title>
<link>https://example.com/research/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/research/</guid>
<description></description>
</item>
<item>
<title>Tour</title>
<link>https://example.com/tour/</link>
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
<guid>https://example.com/tour/</guid>
<description></description>
</item>
</channel>
</rss>