Search results for "Rotamer"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
113	Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink	Rotamer-Pair Energy Calculations Using a Trie Data Structure.	WABI	2005	DBLP DOI BibTeX RDF
70	Lincong Wang, Bruce Randall Donald	An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings.	CSB	2005	DBLP DOI BibTeX RDF
59	Richard S. Judson	Genetic Algorithms for Protein Structure Prediction.	Encyclopedia of Optimization	2009	DBLP DOI BibTeX RDF	Active site, Primary structure, Tertiary structure, Cartesian coordinates, Internal coordinates, Bond distance, Bond angle, Dihedral angle, Rotamer library, Rotamer, Empirical potential, Nonbonded distance, Optimization, Evolution, Configuration, Conformation, Protein structure, Secondary structure, Free energy, Amino acid
51	Peng Zhou 0003, Xiang Chen, Zhicai Shang	Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Multi-conformation-based quantitative structure-activity relationship, Side-chain conformational space analysis, Rotamer library, Self-consistent mean field theory, Protein-peptide complex, HLA-A*0201-restricted CTL epitope
49	Andrew Leaver-Fay, Jack Snoeyink, Brian Kuhlman	On-the-Fly Rotamer Pair Energy Evaluation in Protein Design.	ISBRA	2008	DBLP DOI BibTeX RDF
43	Martin T. Swain, Graham J. L. Kemp	A CLP Approach to the Protein Side-Chain Placement Problem.	CP	2001	DBLP DOI BibTeX RDF
29	Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen	Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.	RECOMB	2004	DBLP DOI BibTeX RDF	beta structures, beta trefoils, motif recognition, rotamer libraries, threading, protein structure prediction
27	Tareq Hameduh, Michal Mokry, Andrew D. Miller 0003, Zbynek Heger, Yazan Haddad	Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
27	Congzhou M. Sha, Jian Wang 0094, Nikolay V. Dokholyan	Differentiable Rotamer Sampling with Molecular Force Fields.	CoRR	2023	DBLP DOI BibTeX RDF
27	Colin A. Grambow, Hayley Weir, Christian N. Cunningham, Tommaso Biancalani, Kangway V. Chuang	CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning.	CoRR	2023	DBLP DOI BibTeX RDF
27	Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng 0001, Jianzhu Ma	Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction.	ICLR	2023	DBLP BibTeX RDF
27	Reagan J. Meredith, Luke Sernau, Anthony S. Serianni	MA'AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
27	Yufeng Liu, Lu Zhang, Weilun Wang, Min Zhu, Chenchen Wang, Fudong Li 0010, Jiahai Zhang, Houqiang Li, Quan Chen, Haiyan Liu	Publisher Correction: Rotamer-free protein sequence design based on deep learning and self-consistency.	Nat. Comput. Sci.	2022	DBLP DOI BibTeX RDF
27	Yufeng Liu, Lu Zhang, Weilun Wang, Min Zhu, Chenchen Wang, Fudong Li 0010, Jiahai Zhang, Houqiang Li, Quan Chen, Haiyan Liu	Rotamer-free protein sequence design based on deep learning and self-consistency.	Nat. Comput. Sci.	2022	DBLP DOI BibTeX RDF
27	Xiaoqiang Huang, Robin Pearce, Yang Zhang 0040	Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
27	Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald	LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.	J. Comput. Biol.	2017	DBLP DOI BibTeX RDF
27	Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald	LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency.	RECOMB	2016	DBLP DOI BibTeX RDF
27	Joshua Pottel, Nicolas Moitessier	Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering.	J. Chem. Inf. Model.	2015	DBLP DOI BibTeX RDF
27	Sandeepkumar Kothiwale, Jeffrey L. Mendenhall, Jens Meiler	BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library.	J. Cheminformatics	2015	DBLP DOI BibTeX RDF
27	Sara E. Hernandez-Ayon, Carlos A. Brizuela	Designing rotamer libraries based on pairs of consecutive residues: A preliminary analysis.	BIBM	2015	DBLP DOI BibTeX RDF
27	Jungkap Park, Kazuhiro Saitou	ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.	BMC Bioinform.	2014	DBLP DOI BibTeX RDF
27	María Larriva, Antonio Rey	Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations.	J. Chem. Inf. Model.	2014	DBLP DOI BibTeX RDF
27	Hiroshi C. Watanabe, Marcus Elstner, Thomas Steinbrecher	Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics.	J. Comput. Chem.	2013	DBLP DOI BibTeX RDF
27	Francis Gaudreault, Matthieu Chartier, Rafael Najmanovich	Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding.	Bioinform.	2012	DBLP DOI BibTeX RDF
27	Md Shariful Bhuyan, Xin Gao 0001	A protein-dependent side-chain rotamer library.	BMC Bioinform.	2011	DBLP DOI BibTeX RDF
27	Yang Cao, Lin Song, Zhichao Miao, Yun Hu, Liqing Tian, Taijiao Jiang	Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.	Bioinform.	2011	DBLP DOI BibTeX RDF
27	Jianyang Zeng 0001, Kyle E. Roberts, Pei Zhou 0001, Bruce Randall Donald	A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data.	J. Comput. Biol.	2011	DBLP DOI BibTeX RDF
27	Jianyang Zeng 0001, Kyle E. Roberts, Pei Zhou 0001, Bruce Randall Donald	A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data.	RECOMB	2011	DBLP DOI BibTeX RDF
27	Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga	Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
27	Urszula Kozlowska, Adam Liwo, Harold A. Scheraga	Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
27	Feng Ding 0002, Shuangye Yin, Nikolay V. Dokholyan	Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands.	J. Chem. Inf. Model.	2010	DBLP DOI BibTeX RDF
27	Katalin E. Kövér, Tamás Beke, András Lipták, András Perczel	Combined NMR three-bond scalar coupling measurements and QM calculations to calculate OH-rotamer equilibrium of polyalcohols.	J. Comput. Chem.	2009	DBLP DOI BibTeX RDF
27	Yifan Song, Junjun Mao, Marilyn R. Gunner	MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling.	J. Comput. Chem.	2009	DBLP DOI BibTeX RDF
27	Eun-Jong Hong, Shaun M. Lippow, Bruce Tidor, Tomás Lozano-Pérez	Rotamer optimization for protein design through MAP estimation and problem-size reduction.	J. Comput. Chem.	2009	DBLP DOI BibTeX RDF
27	Luis P. B. Scott, Jorge Chahine, José R. Ruggiero	Predicting peptides structure with solvation potential and rotamer library dependent of the backbone.	Appl. Math. Comput.	2008	DBLP DOI BibTeX RDF
27	Eun-Jong Hong	Exact rotamer optimization for computational protein design.		2008	RDF
27	Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink, Brian Kuhlman	Maintaining solvent accessible surface area under rotamer substitution for protein design.	J. Comput. Chem.	2007	DBLP DOI BibTeX RDF
27	Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvão, Tom L. Blundell	Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.	Bioinform.	2007	DBLP DOI BibTeX RDF
27	Wei Xie, Nikolaos V. Sahinidis	Residue-rotamer-reduction algorithm for the protein side-chain conformation problem.	Bioinform.	2006	DBLP DOI BibTeX RDF
27	D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce	Exact rotamer optimization for protein design.	J. Comput. Chem.	2003	DBLP DOI BibTeX RDF
27	Kerstin Koch, Frank Zöllner 0001, Steffen Neumann, Franz Kummert, Gerhard Sagerer	Comparing bound and unbound protein structures using energy calculation and rotamer statistics.	Silico Biol.	2002	DBLP BibTeX RDF
27	Kerstin Koch, Frank Zöllner 0001, Gerhard Sagerer	Building a new Rotamer Library for Protein-Protein Docking using energy calculations and statistical approaches.	German Conference on Bioinformatics	2001	DBLP BibTeX RDF
27	Jacquelyn S. Fetrow, George Berg	Using Information Theory to Discover Side Chain Rotamer Classes: Analysis of the Effects of Local Backbone Structure.	Pacific Symposium on Biocomputing	1999	DBLP BibTeX RDF
27	Alexander Hinneburg, Daniel A. Keim, Wolfgang Brandt	Detecting relationships between amino acid residue sequences and 3D protein structures based on a new class of rotamer libraries.	German Conference on Bioinformatics	1998	DBLP BibTeX RDF
21	José C. Calvo, Julio Ortega Lopera, Mancia Anguita, José M. Urquiza, J. P. Florido	Protein Structure Prediction by Evolutionary Multi-objective Optimization: Search Space Reduction by Using Rotamers.	IWANN (1)	2009	DBLP DOI BibTeX RDF
21	Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu 0001	An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing.	Algorithmica	2008	DBLP DOI BibTeX RDF	Side-chain, Algorithm, Protein threading, Backbone
21	Ponnadurai Ramasami	First Principle Gas Phase Study of the Trans and Gauche Rotamers of 1, 2-Diisocyanoethane, 1, 2-Diisocyanodisilane and Isocyano(isocyanomethyl)silane.	ICCS (2)	2008	DBLP DOI BibTeX RDF	1 & 2-diisocyanoethane, 1 & 2-diisocyanodisilane and isocyano (isocyano-methyl)silane, MP2, DFT/B3LYP, energy difference, rotational barrier
21	Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu 0001	An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing.	Algorithmica	2007	DBLP DOI BibTeX RDF
21	Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald	A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles.	RECOMB	2006	DBLP DOI BibTeX RDF
21	Ket Fah Chong, Hon Wai Leong	An extension of dead end elimination for protein side-chain conformation using merge-decoupling.	SAC	2006	DBLP DOI BibTeX RDF	protein side chain conformation, algorithm
21	Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald	A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.	RECOMB	2004	DBLP DOI BibTeX RDF	enzyme design, fluorescence binding assay, molecular ensemble, non-ribosomal peptide synthetase, protein flexibility, protein-ligand binding, protein design
21	Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller 0008	A combinatorial approach to protein docking with flexible side-chains.	RECOMB	2000	DBLP DOI BibTeX RDF