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Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

Hao Fan, Dina Schneidman-Duhovny, John J. Irwin, Guangqiang Dong, Brian K. Shoichet, Andrej Sali
2011 Journal of Chemical Information and Modeling  
The statistical potentials are available through the Integrative Modeling Platform (IMP) software package , shoichet@cgl.ucsf.edu.  ...  Applications in structural biology and medicinal chemistry require protein-ligand scoring functions for two distinct tasks: (i) ranking different poses of a small molecule in a protein binding site; and  ...  Jiang Zhu for discussion about the theory used for computing statistical potentials, and Dr. Daniel Russel and Keren Lasker for implementation of the scoring function in IMP.  ... 
doi:10.1021/ci200377u pmid:22014038 pmcid:PMC3246566 fatcat:ylmrfjw3afbinlq5shilkymxxi

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions

Zheng Zheng, Kenneth M. Merz
2013 Journal of Chemical Information and Modeling  
We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential  ...  In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB).  ...  Acknowledgments We would like to thank the NIH (GM044974 and GM066859) for supporting the present research. Dr. Michael Weaver is also acknowledged for numerous helpful discussions.  ... 
doi:10.1021/ci300619x pmid:23560465 pmcid:PMC3686284 fatcat:u23i37ezizexdcqbh4g3nr5nii

Interactions in Native Binding Sites Cause a Large Change in Protein Dynamics

Dengming Ming, Michael E. Wall
2006 Journal of Molecular Biology  
In DPA, a protein is decorated with surface points that interact with neighboring protein atoms, and D x is calculated for each of the points in a coarse-grained model of protein vibrations.  ...  We use DPA to examine hundreds of protein structures from a standard small-molecule docking test set, and find that ligand-binding sites have elevated values of D x : for 95% of proteins, the probability  ...  The measure D x (m ) is called the allosteric potential of the interaction of point m with the protein.  ... 
doi:10.1016/j.jmb.2006.01.097 pmid:16513135 fatcat:ge6pdecvqjhrblwce24axj7bdi

Statistical potentials and scoring functions applied to protein–ligand binding

Holger Gohlke, Gerhard Klebe
2001 Current Opinion in Structural Biology  
In virtual screening, small-molecule ligands are docked into protein binding sites and their binding affinity is predicted.  ...  Knowledge-based, regression-based and first-principle-based methods have been developed to rank computer-generated binding modes.  ...  Protein-ligand complexes modeled using a particular input potential were selected to construct databases from which statistical protein-ligand potentials were derived.  ... 
doi:10.1016/s0959-440x(00)00195-0 pmid:11297933 fatcat:wyxafmddsndflgkz6d3hizr344

MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes

N. Kumar, D. Mohanty
2007 Nucleic Acids Research  
MODPROPEP provides a number of userfriendly interfaces for visualizing the structure of the modeled protein-peptide complexes and analyzing the contacts made by the modeled peptide ligand in the substrate-binding  ...  these inter-molecular contacts using residue-based statistical pair potentials.  ...  Dunbrack Jr for allowing the use of SCWRL for modeling of side chains.  ... 
doi:10.1093/nar/gkm266 pmid:17478500 pmcid:PMC1933231 fatcat:74jtt2fb5jertin2q7fyuxfkxa

Knowledge-based scoring function to predict protein-ligand interactions

Holger Gohlke, Manfred Hendlich, Gerhard Klebe
2000 Journal of Molecular Biology  
) dependent singlet preferences for protein and ligand atoms.  ...  For two test sets of 91 and 68 protein-ligand complexes, taken from the Protein Data Bank (PDB), the calculated score recognizes poses generated by FlexX deviating <2 A Ê from the crystal structure on  ...  Acknowledgments This work was performed as part of the RELIMO-Project (grant number 0311619) funded by the German Federal Ministry for Education, Science, Research, and Technology (BMBF).  ... 
doi:10.1006/jmbi.1999.3371 pmid:10623530 fatcat:24uufzhrbvbtvmnrabxn5rkui4

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions

Andrea Bazzoli, Simon P. Kelow, John Karanicolas, Yang Zhang
2015 PLoS ONE  
(B) The variant of the score12 energy function that was developed specifically for modeling protein-ligand interactions, score12_ligand, offers improved performance over score12 (p = 0.001).  ...  Protein-protein interactions are among today's most exciting and promising targets for therapeutic intervention.  ...  We are grateful to OpenEye Scientific Software (Sante Fe, NM) for providing an academic license for the use of FRED, QUACPAC, and OMEGA.  ... 
doi:10.1371/journal.pone.0140359 pmid:26484863 pmcid:PMC4617380 fatcat:teggu64z4rcf7o3s5tiaeu5mim

A coarse-grained force field for Protein–RNA docking

Piotr Setny, Martin Zacharias
2011 Nucleic Acids Research  
Here, we present a coarse-grained force field for protein-RNA docking, implemented within the framework of the ATTRACT program.  ...  Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often  ...  RESULTS AND DISCUSSION Potential parameters The obtained statistical potentials provide a valuable characterization of the assumed interaction model (see Supplementary Data for the corresponding plots  ... 
doi:10.1093/nar/gkr636 pmid:21846771 pmcid:PMC3241652 fatcat:6qqaspow7vdcpb5rxyamolx354

Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry

Uthaman Gowthaman, Mannu Jayakanthan, Durai Sundar
2008 BMC Bioinformatics  
All ligands showed favorable interactions and most of them seemed to bind to hydrophobic amino acids Ala34, Trp36, Cys37, Cys40, His39, Thr68 and Phe80.  ...  Interestingly we found that number of docked clusters with each ligand varies in the range of five to eight and conveys that the binding specificity of each inhibitor varies for PDI.  ...  Acknowledgements Research in the laboratory of DS is supported by grants from Department of Biotechnology (DBT), Department of Science and Technology (DST) and Department of Information Technology (DIT  ... 
doi:10.1186/1471-2105-9-s12-s14 pmid:19091013 pmcid:PMC2638154 fatcat:ieb6v6obqnbulgki2scp4uvere

ANTI-INFECTIOUS DRUG REPURPOSING USING AN INTEGRATED CHEMICAL GENOMICS AND STRUCTURAL SYSTEMS BIOLOGY APPROACH

CLARA NG, RUTH HAUPTMAN, YINLIANG ZHANG, PHILIP E. BOURNE, LEI XIE
2013 Biocomputing 2014  
This study demonstrates the potential of an integrative chemical genomics and structural systems biology approach to drug repurposing.  ...  Although drug repurposing is a promising solution for accelerating the drug development process, its application to anti-infectious drug discovery is limited by the scope of existing phenotype-, ligand  ...  Acknowledgments This research was supported, in part, under National Science Foundation Grants CNS-0958379 and CNS-0855217 and the City University of New York High Performance Computing Center at the College  ... 
doi:10.1142/9789814583220_0014 fatcat:eignrpg5qnd3llhv72q443hlfu

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database

Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li
2017 Nucleic Acids Research  
159 druggable pharmacophore models and 51 431 ligandable pharmacophore models.  ...  In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores.  ...  It refers to a proteinligand interaction pattern corresponding to a desired pharmacological effect and can be considered as the largest common denominator shared by a set of active molecules.  ... 
doi:10.1093/nar/gkx374 pmid:28472422 pmcid:PMC5793840 fatcat:amn26acpsncfpjva22uvwp6q5u

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

Sheng-You Huang, Sam Z. Grinter, Xiaoqin Zou
2010 Physical Chemistry, Chemical Physics - PCCP  
Despite considerable success, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking.  ...  The commonly-used assessment criteria and publicly available protein-ligand databases for performance evaluation of the scoring functions have also been presented and discussed.  ...  Her research interests are physical modeling of protein-ligand and protein-protein interactions, structure-function relationship of membrane proteins, and structure-based drug design.  ... 
doi:10.1039/c0cp00151a pmid:20730182 fatcat:vuvan67jebczvdn76izf56mz74

Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials

Andreas Evers, Holger Gohlke, Gerhard Klebe
2003 Journal of Molecular Biology  
Subsequently, the most favourable models are selected by ranking the interactions between the ligands and the generated pockets using these potentials.  ...  Thus optimised models can be used for structure-based drug design and virtual screening. In a first step, ligands are docked into an averaged ensemble of crude homology models of the target protein.  ...  Podjarny (IGBMC, Illkirch, France) for providing the coordinates of the crystal structure of the IDD594 complex.  ... 
doi:10.1016/j.jmb.2003.09.032 pmid:14607122 fatcat:fo23nw5r5zhpzdrzzt4pnfmk5y

STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS [chapter]

LAURA PÉREZ-CANO, ALBERT SOLERNOU, CARLES PONS, JUAN FERNÁNDEZ-RECIO
2009 Biocomputing 2010  
In this study we have extracted new pairwise residue-ribonucleotide interface propensities for protein-RNA, which can be used as statistical potentials for scoring of protein-RNA docking poses.  ...  Despite the importance of protein-RNA interactions in the cellular context, the number of available protein-RNA complex structures is still much lower than those of other biomolecules.  ...  Acknowledgments This work is supported by grant BIO2008-02882 from Plan Nacional I+D+i (Spanish Ministry of Science). LP-C is recipient of an FPU fellowship from the Spanish Ministry of Science.  ... 
doi:10.1142/9789814295291_0031 fatcat:jkber7akwvgbpk2ewly46glaae

Application of asymmetric statistical potentials to antibody-protein docking

R. Brenke, D. R. Hall, G.-Y. Chuang, S. R. Comeau, T. Bohnuud, D. Beglov, O. Schueler-Furman, S. Vajda, D. Kozakov
2012 Bioinformatics  
Motivation: An effective docking algorithm for antibody-protein antigen complex prediction is an important first step toward design of biologics and vaccines.  ...  Interaction statistics were extracted from antibody-protein complexes under the assumption that a particular atom on the antibody is different from the same atom on the antigen protein.  ...  ACKNOWLEDGEMENTS For the CPU time used for this article, the authors thank the Boston University Scientific Computing and Visualization Center for the opportunity of running the PIPER program on the Blue  ... 
doi:10.1093/bioinformatics/bts493 pmid:23053206 pmcid:PMC3467743 fatcat:ad5h635pnrb63o6ymfrququpne
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