csb.pitt.edu

pocketquery.csb.pitt.edu

PocketQuery

PocketQuery is currently down while a corrupted database gets repaired. Please check back later. PPI Inhibitor Starting Points from PPI Structure. For best results, please use Firefox. If you have a modern browser, Java is not. The top ranked cluster in this example screen. Of the p53/MDM2 interface, an anti-cancer target, is a proven starting point for drug discovery. PocketQuery is a web service for interactively exploring not only hot spot and anchor residues, but hot. From the Camacho Lab.

pharmit.csb.pitt.edu

pharmit: interactive exploration of chemical space

Please let us know. We are in need of letters of support. Interactive exploration of chemical space. Virtual screening in your browser. Submit your own chemical libraries. Log in to manage libraries. Log in as guest. Publicly accessible user-contributed libraries. If you find this site useful please cite Pharmit: interactive exploration of chemical space. David Ryan Koes, Charles Yuan and the University of Pittsburgh.

bits.csb.pitt.edu

David Ryan Koes

David Ryan Koes, PhD. Removing barriers to computational drug discovery one bit at a time. I have a PhD in Computer Science from Carnegie Mellon. And am an Assistant Professor in the Department of Computational and Systems Biology. At the University of Pittsburgh. My research is to develop novel computational algorithms and build full-scale systems to support rapid and inexpensive drug discovery while simultaneously applying these methods to develop novel therapeutics. Pittsburgh, PA 15260.

gnm.csb.pitt.edu

Dynomics Portal 1.0 - Dynamics Proteomics and Beyond

Computational and Systems Biology. What is the Dynomics. Ynamics) evaluates the equilibrium dynamics of biomolecular systems using structural data. At the core of o. ENM are two elastic network models (ENM): the Gaussian Network Model ( i. And the Anisotropic Network Model ( ANM 2.0. Distinctive features of o. ENM include: evaluation of the effect of environment, estimation of functional sites, and mapping ENM predictions onto their full-atomic representations. With biological assembly (unit). Awards #5R...

gnmdb.csb.pitt.edu

iGNM - Online service for Gaussian Network Model

Computational and Systems Biology. What is the GNM DB? Which questions can be answered? Several studies in the last decade have drawn attention to the significance of intrinsic dynamics as a major determinant of the mechanism of action of proteins and their complexes (1-5). Intrinsic dynamics refers to conformational changes intrinsically favored by 3D structure, which often underlie the adaptation of biomolecules to functional interactions (6). Or which ones provide adequate flexibility. 2 Dobbins,S&#46...

3dmol.csb.pitt.edu

3Dmol.js

A modern, object-oriented JavaScript library for visualizing molecular data. View structures through a declarative URL interface. Embed molecular viewers in webpages with two lines of code. Develop web applications using a full featured API.

balestra.csb.pitt.edu

BalestraWeb

Enter Drug ID (e.g. "Loxapine" or "DB00408"):. ID and some common drug names. Enter Target ID (e.g. "ADRB2" or "BE0000694"):. Recognizes ID from DrugBank. No of Predictions (1 to 100):. Data on protein-drug interactions are rapidly increasing and being collected in databases such as DrugBank. BalestraWeb addresses this need by learning a probabilistic latent factor model of drug-target interactions and enabling users to predict the interactions of:. BalestraWeb is built using GraphLab. Funding: Support f...

anm.csb.pitt.edu

ANM 2.0 (home)

Odel Web Server 2.0 (2014). What's new in this version? Enter the PDB id of your protein. Submit your own protein. Default: all polypeptide chains). For multi-model files such as from NMR). For interaction between Cα atoms (&#197). Enter distance weight factor. For interaction between Cα atoms. Enter number of normal modes to calculate. Enter engine for eigensolver.

anchorquery.csb.pitt.edu

AnchorQuery™ Web Page

Is a specialized pharmacophore. Search technology that brings interactive virtual screening of novel protein-protein inhibitors to the desktop. Try one of the interactive examples. Or read the Getting Started. Guide in the User Manual. To search for a custom pharmacophore. Anchor analogs (F,L,W,V,Y,D,E). 2,002,551,771. Search Anchor Biased Library. Extract PPI inhibitor starting point pharmacophores from PPI structure with PocketQuery. User Guide and Forum. This interaction is an. Is an enzyme complex in...

prody.csb.pitt.edu

ProDy — Protein Dynamics and Sequence Analysis

Dynamics of p38 MAP kinase inferred from a structural ensemble using PCA is compared to intrinsic dynamics of the protein modeled using ANM. See PCA of X-ray structures. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.