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Optimized atomic statistical potentials: assessment of protein interfaces and loops

Guang Qiang Dong, Hao Fan, Dina Schneidman-Duhovny, Ben Webb, Andrej Sali
2013 Computer applications in the biosciences : CABIOS  
To demonstrate this general approach, we computed statistical potentials for protein-protein docking (SOAP-PP) and loop modeling (SOAP-Loop).  ...  Motivation: Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules  ...  RESULTS Scoring protein-protein interfaces SOAP-PP is an atomic statistical potential for assessing a binary protein interface, computed with our Bayesian framework by optimizing its accuracy on the  ... 
doi:10.1093/bioinformatics/btt560 pmid:24078704 pmcid:PMC3842762 fatcat:4pbjmhgq2ngw5b75bgkle6gtmu

Unbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential [article]

Song Liu, Chi Zhang, Yaoqi Zhou
2004 arXiv   pre-print
A newly developed statistical pair potential based on Distance-scaled Finite Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking structure selections.  ...  optimized for docking.  ...  This work was supported by NIH (R01 GM 966049 and R01 GM 068530), a grant from HHMI to SUNY Buffalo and by the Center for Computational Research and the Keck Center for Computational Biology at SUNY Buffalo  ... 
arXiv:q-bio/0406025v2 fatcat:7lnstltbdnbjnbnizvo3wy3d3q

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

Shiyong Liu, Ilya A Vakser
2011 BMC Bioinformatics  
An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom) pairs in the non-interaction state.  ...  Conclusions: A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets.  ...  Acknowledgements The authors thank Anatoly Ruvinsky for helpful comments and suggestions. The authors are grateful to Yaoqi Zhou for providing DCOMPLEX program.  ... 
doi:10.1186/1471-2105-12-280 pmid:21745398 pmcid:PMC3145612 fatcat:mjud4onfz5hcxhduc4nswg5r5q

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

Y. Chen
2004 Nucleic Acids Research  
By incorporating the new hydrogen-bonding potential into a physical model of protein-RNA interfaces with full atom representation, we were able to recover native amino acids at protein-RNA interfaces.  ...  of protein-DNA and protein-RNA complexes.  ...  at protein-RNA interfaces, and Dr Jens Meiler for use of the protein-ligand docking module of ROSETTA to generate protein-RNA decoy sets.  ... 
doi:10.1093/nar/gkh785 pmid:15459285 pmcid:PMC521638 fatcat:wz3ufzfg2zac3fezzvgxv4g4cq

Statistical potential for assessment and prediction of protein structures

Min-yi Shen, Andrej Sali
2006 Protein Science  
Using the probability theory, we derive an atomic distancedependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein  ...  To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling,  ...  We acknowledge NIH R01 GM54762 and The Sandler Family Supporting Foundation for funding, as well as IBM and Intel for computer hardware.  ... 
doi:10.1110/ps.062416606 pmid:17075131 pmcid:PMC2242414 fatcat:5ks2ivlxingndjlqsck5w3g6pm

BCL::Score—Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

Nils Woetzel, Mert Karakaş, Rene Staritzbichler, Ralf Müller, Brian E. Weiner, Jens Meiler, Charlotte M. Deane
2012 PLoS ONE  
loop length, radius of gyration, contact order and secondary structure prediction agreement are defined.  ...  Pairing of b-strands defines the topology of b-sheets. The packing of side chains between a-helices and b-sheets defines the majority of the protein core.  ...  Acknowledgments We thank the CSB and ACCRE staff at Vanderbilt for computer support. Author Contributions  ... 
doi:10.1371/journal.pone.0049242 pmid:23173051 pmcid:PMC3500277 fatcat:oz7qrxi4gbfftg3b3ugm6vdftq

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

J. Shimada, A.V. Ishchenko, E.I. Shakhnovich
2008 Protein Science  
The most successful procedure was applied to derive an atom-atom potential for real protein-ligand complexes.  ...  We then tested several different modifications to such potentials and evaluated their performance on their ability to reconstruct the input potential using the statistical information available from a  ...  Acknowledgments We would like to thank Professor Steve Elick of Cornell University for generously providing us with unpublished structures and binding constants for several PNP-inhibitor complexes.  ... 
doi:10.1110/ps.9.4.765 pmid:10794420 pmcid:PMC2144609 fatcat:chxehj5wd5frlaysct2ul64o2y

The Dependence of All-Atom Statistical Potentials on Structural Training Database

Chi Zhang, Song Liu, Hongyi Zhou, Yaoqi Zhou
2004 Biophysical Journal  
They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP (atomic knowledge-based potential), and DFIRE (statistical potential based on distance-scaled finite  ...  Here, two high-resolution, low-sequence-identity structural databases of 333 a-proteins and 271 b-proteins were built for examining the database dependence of three all-atom statistical energy functions  ...  One is the potential between C b atoms of Leu and Asp and the other is between backbone N atom of Val and O atom of Trp.  ... 
doi:10.1529/biophysj.103.035998 pmid:15189839 pmcid:PMC1304244 fatcat:ojxwfglennfobf22xfpcw4l5ki

Exploring the potential of 3D Zernike descriptors and SVM for protein–protein interface prediction

Sebastian Daberdaku, Carlo Ferrari
2018 BMC Bioinformatics  
The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount  ...  The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins  ...  Funding This research has been partially supported by the University of Padova project CPDR150813/15 "Models and Algorithms for Protein-Protein Docking".  ... 
doi:10.1186/s12859-018-2043-3 pmid:29409446 pmcid:PMC5802066 fatcat:srbkrq4ke5hnzauokcbpmldrnq

Protein sequence design with a learned potential [article]

Namrata Anand, Raphael Ryuichi Eguchi, Alexander Derry, Russ B Altman, Possu Huang
2020 bioRxiv   pre-print
In this study, we propose a novel method for fixed-backbone protein sequence design using a learned deep neural network potential.  ...  The primary challenge of fixed-backbone protein sequence design is to find a distribution of sequences that fold to the backbone of interest.  ...  We thank Wen Torng, Sergey Ovchinnikov, Alex Chu, and Christian Choe for helpful discussion, and Frank DiMaio for providing a set of decoys from which we selected test case structures.  ... 
doi:10.1101/2020.01.06.895466 fatcat:qouaaoxqmnacbgadewfh7uor24

Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design [chapter]

Alexandre V. Morozov, Tanja Kortemme
2005 Advances in Protein Chemistry  
Acknowledgments We thank David Baker and many members of the Baker laboratory for stimulating discussions and insights.  ...  A.V.M. is supported by a postdoctoral fellowship from the Leukemia and Lymphoma Society. T.K. acknowledges support from the Human Frontier Science Program.  ...  Recovery of native sequences in protein-protein interfaces.  ... 
doi:10.1016/s0065-3233(05)72001-5 pmid:16581371 fatcat:m6lf6vjwuzfplbf3xn3rxrjupa

Structure ofStaphylococcus aureusadenylosuccinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery

Paul K. Fyfe, Alice Dawson, Marie-Theres Hutchison, Scott Cameron, William N. Hunter
2010 Acta Crystallographica Section D: Biological Crystallography  
The distinct subunit–subunit interfaces may provide a potential area to target by exploiting the observation that creation of the enzyme active site is dependent on oligomerization.  ...  PurB catalyzes reactions that support the provision of purines and the control of AMP/fumarate levels.  ...  Selective inhibition of PurB offers the possibility of new therapies targeting a range of microbial infections and structural studies provide useful data to assess the potential of this protein for such  ... 
doi:10.1107/s0907444910020081 pmid:20693687 pmcid:PMC2917274 fatcat:f5j4dymt45a77irl43cckgudn4

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

Gwo-Yu Chuang, Dima Kozakov, Ryan Brenke, Stephen R. Comeau, Sandor Vajda
2008 Biophysical Journal  
of the interface.  ...  The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as  ...  Here we use the 18 atom types as introduced for the atomic contact potential (ACP) (24) , an atom-level extension of the Miyazawa-Jernigan potential (5), but note that optimizing atom type selection may  ... 
doi:10.1529/biophysj.108.135814 pmid:18676649 pmcid:PMC2567923 fatcat:hjiovnmzljhizhilldaaf4yk2u

A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations

Zongan Wang, John M Jumper, Sheng Wang, Karl F Freed, Tobin R Sosnick
2018 Biophysical Journal  
We use the statistics of a large and curated training set of transmembrane helical proteins to develop a knowledge-based potential that accounts for the dependence on both the depth of burial of the protein  ...  The potential is applied to the mechanosensing MscL channel in membranes of varying thickness and curvature, as well as to the prediction of protein structure.  ...  A web server is available to insert helical transmembrane protein models into membranes and run Upside simulations of the inserted model as rigid body to generate an ensemble of orientations: http://sosnick  ... 
doi:10.1016/j.bpj.2018.10.012 pmid:30413241 pmcid:PMC6303381 fatcat:m7f72c75xvhaxb5utqv42byl74

DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking

Dennis M. Krüger, José Ignacio Garzón, Pablo Chacón, Holger Gohlke, Paolo Carloni
2014 PLoS ONE  
The distance-dependent knowledge-based DrugScore PPI potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated  ...  as a scoring and objective function for the structure prediction of protein-protein complexes.  ...  Author Contributions Conceived and designed the experiments: HG DMK. Performed the experiments: DMK JIG. Analyzed the data: DMK JIG PC HG. Wrote the paper: DMK PC HG.  ... 
doi:10.1371/journal.pone.0089466 pmid:24586799 pmcid:PMC3931789 fatcat:ng4fpcbhozaijjmo3xsfcuux4y
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