Search results for "Pfam"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
59	Cyril Allauzen, Mehryar Mohri, Ameet Talwalkar	Sequence kernels for predicting protein essentiality.	ICML	2008	DBLP DOI BibTeX RDF
50	Thomas Lingner, Peter Meinicke	Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach.	WABI	2008	DBLP DOI BibTeX RDF	Pfam, target set reduction, machine learning, large-scale, protein classification, multi-class, metagenomics, homology search, protein function prediction, multi-label
50	Mihaela Pertea, Steven Salzberg	Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding.	WABI	2007	DBLP DOI BibTeX RDF	Pfam, GHMM, ab intio gene finding, protein domain, profile HMM
40	Congzhong Cai, Qianfei Yuan, Hanguang Xiao, Xinghua Liu, Lianyi Han, Yu Zong Chen	Prediction of Transmembrane Proteins from Their Primary Sequence by Support Vector Machine Approach.	ICIC (3)	2006	DBLP DOI BibTeX RDF
40	Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik	Screening for Ortholog Clusters Using Multipartite Graph Clustering by Quasi-Concave Set Function Optimization.	RSFDGrC (2)	2005	DBLP DOI BibTeX RDF
40	David A. Lee, Alastair Grant, Ian Sillitoe, Mark Dibley, Juan Garcia Ranea, Christine A. Orengo	A structural perspective on genome evolution.	RECOMB	2004	DBLP DOI BibTeX RDF
40	Byung-Hoon Park, George Ostrouchov, Gong-Xin Yu, Al Geist, Andrey Gorin, Nagiza F. Samatova	Inference of Protein-Protein Interactions by Unlikely Profile Pair.	ICDM	2003	DBLP DOI BibTeX RDF
31	Minghua Deng, Ting Chen 0006, Fengzhu Sun	An integrated probabilistic model for functional prediction of proteins.	RECOMB	2003	DBLP DOI BibTeX RDF	function prediction, pfam domain, Markov random field, protein-protein interaction, Gibbs sampler
27	Zhen Wah Tan, Wei-Ven Tee, Enrico Guarnera, Igor N. Berezovsky	AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
27	Qingting Wei, Hong Zou, Cuncong Zhong, Jianfeng Xu	RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families.	J. Bioinform. Comput. Biol.	2022	DBLP DOI BibTeX RDF
27	Elena Tea Russo, Alessandro Laio, Marco Punta	Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation.	BMC Bioinform.	2021	DBLP DOI BibTeX RDF
27	Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman	Pfam: The protein families database in 2021.	Nucleic Acids Res.	2021	DBLP DOI BibTeX RDF
27	Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurelien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn	The Pfam protein families database in 2019.	Nucleic Acids Res.	2019	DBLP DOI BibTeX RDF
27	Frank Keul, Martin Hess, Michael Goesele, Kay Hamacher	PFASUM: a substitution matrix from Pfam structural alignments.	BMC Bioinform.	2017	DBLP DOI BibTeX RDF
27	Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie	ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.	BMC Bioinform.	2017	DBLP DOI BibTeX RDF
27	Mirco Michel, Marcin J. Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson	Predicting accurate contacts in thousands of Pfam domain families using PconsC3.	Bioinform.	2017	DBLP DOI BibTeX RDF
27	Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie	Associating Gene Ontology Terms with Pfam Protein Domains.	IWBBIO (2)	2017	DBLP DOI BibTeX RDF
27	Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman	The Pfam protein families database: towards a more sustainable future.	Nucleic Acids Res.	2016	DBLP DOI BibTeX RDF
27	Zachary Chiang, Åke Västermark, Marco Punta, Penelope Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier Jr.	The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.	Briefings Bioinform.	2015	DBLP DOI BibTeX RDF
27	Andrew Ndhlovu, Pierre M. Durand, Scott Hazelhurst	EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.	Database J. Biol. Databases Curation	2015	DBLP DOI BibTeX RDF
27	Bachir Balech, Saverio Vicario, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo, Graziano Pesole	MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.	Bioinform.	2015	DBLP DOI BibTeX RDF
27	Felix A. Krüger, Anna Gaulton, Michal Nowotka, John P. Overington	PPDMs - a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.	Bioinform.	2015	DBLP DOI BibTeX RDF
27	Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta	Pfam: the protein families database.	Nucleic Acids Res.	2014	DBLP DOI BibTeX RDF
27	Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman	Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.	BMC Bioinform.	2013	DBLP DOI BibTeX RDF
27	Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta	The challenge of increasing Pfam coverage of the human proteome.	Database J. Biol. Databases Curation	2013	DBLP DOI BibTeX RDF
27	Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta	The challenge of increasing Pfam coverage of the human proteome.	Database J. Biol. Databases Curation	2013	DBLP DOI BibTeX RDF
27	Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn	The Pfam protein families database.	Nucleic Acids Res.	2012	DBLP DOI BibTeX RDF
27	Qifang Xu, Roland L. Dunbrack Jr.	Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.	Bioinform.	2012	DBLP DOI BibTeX RDF
27	Gustavo A. Arango-Argoty, José Francisco Ruiz-Muñoz, Jorge Alberto Jaramillo-Garzón, César Germán Castellanos-Domínguez	An adaptation of Pfam profiles to predict protein sub-cellular localization in Gram positive bacteria.	EMBC	2012	DBLP DOI BibTeX RDF
27	Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman	The Pfam protein families database.	Nucleic Acids Res.	2010	DBLP DOI BibTeX RDF
27	Asif U. Tamuri, Roman A. Laskowski	ArchSchema: a tool for interactive graphing of related Pfam domain architectures.	Bioinform.	2010	DBLP DOI BibTeX RDF
27	Nalin C. W. Goonesekere, Krysten Shipely, Kevin O'Connor	The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam.	Comput. Biol. Chem.	2010	DBLP DOI BibTeX RDF
27	Stephen John Sammut, Robert D. Finn, Alex Bateman	Pfam 10 years on: 10 000 families and still growing.	Briefings Bioinform.	2008	DBLP DOI BibTeX RDF
27	Robert D. Finn, John G. Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman	The Pfam protein families database.	Nucleic Acids Res.	2008	DBLP DOI BibTeX RDF
27	Jaina Mistry, Alex Bateman, Robert D. Finn	Predicting active site residue annotations in the Pfam database.	BMC Bioinform.	2007	DBLP DOI BibTeX RDF
27	Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman	Pfam: clans, web tools and services.	Nucleic Acids Res.	2006	DBLP DOI BibTeX RDF
27	Elizabeta Bab-Dinitz, Hagay Shmuely, Julie Maupin-Furlow, Jerry Eichler, Boaz Shaanan	Haloferax volcanii PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?	Bioinform.	2006	DBLP DOI BibTeX RDF
27	Ana Gabriela Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. M. Strauss, Luis M. Rocha	Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families.	Pacific Symposium on Biocomputing	2006	DBLP BibTeX RDF
27	Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam	SledgeHMMER: a web server for batch searching the Pfam database.	Nucleic Acids Res.	2004	DBLP DOI BibTeX RDF
27	Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy	The Pfam protein families database.	Nucleic Acids Res.	2004	DBLP DOI BibTeX RDF
27	Edward de Oliveira Ribeiro, Gustavo G. Zerlotini, Irving Lopes, Victor Ribeiro, Alba Cristina Magalhaes Alves de Melo, Maria Emília Telles Walter, Marcos Motta	Rede BIOFOCO: A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation.	WOB	2004	DBLP BibTeX RDF
27	David J. Studholme, Neil D. Rawlings, Alan J. Barrett, Alex Bateman	A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.	BMC Bioinform.	2003	DBLP DOI BibTeX RDF
27	Weirong Zhu, Yanwei Niu, Jizhu Lu, Guang R. Gao	Implementing Parallel Hmm-pfam on the EARTH Multithreaded Architecture.	CSB	2003	DBLP DOI BibTeX RDF
27	Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer	The Pfam Protein Families Database.	Nucleic Acids Res.	2002	DBLP DOI BibTeX RDF
27	Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer	The Pfam Protein Families Database.	Nucleic Acids Res.	2000	DBLP DOI BibTeX RDF
27	Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer	Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.	Nucleic Acids Res.	1999	DBLP DOI BibTeX RDF
27	Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin	Pfam: multiple sequence alignments and HMM-profiles of protein domains.	Nucleic Acids Res.	1998	DBLP DOI BibTeX RDF
20	Karen T. Girão, Fátima C. E. Oliveira, Kaio M. Farias, Italo M. C. Maia, Samara C. Silva, Carla R. F. Gadelha, Laura D. G. Carneiro, Ana Carolina L. Pacheco, Michel T. Kamimura, Michely C. Diniz, Maria C. Silva, Diana M. Oliveira	Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins.	PRIB	2008	DBLP DOI BibTeX RDF	tetratricopeptide repeat motif, Leishmania proteins, hidden Markov models, Viterbi algorithm, Multi-relational data mining
20	Somesh Jha, Louis Kruger, Vitaly Shmatikov	Towards Practical Privacy for Genomic Computation.	SP	2008	DBLP DOI BibTeX RDF	Privacy, Edit Distance, Genome, Secure Multi-Party Computation, Smith-Waterman
20	Marco Masseroli	Management and Analysis of Genomic Functional and Phenotypic Controlled Annotations to Support Biomedical Investigation and Practice.	IEEE Trans. Inf. Technol. Biomed.	2007	DBLP DOI BibTeX RDF
20	Scooter Willis	Protein CorreLogo: an X3D representation of co-evolving pairs, tertiary structure, ligand binding pockets and protein-protein interactions in protein families.	Web3D	2007	DBLP DOI BibTeX RDF	Protein CorreLogo, mutual information, X3D
20	Margaret Dah-Tsyr Chang, Hao-Teng Chang, Rong-Yuan Huang, Wen-Shyong Tzou, Chih-Hong Liu, Wei-Jun Zhung, Hsien-Wei Wang, Chun-Tien Chang, Tun-Wen Pai	A Database for Prediction of Unique Peptide Motifs as Linear Epitopes.	ISBRA	2007	DBLP DOI BibTeX RDF	unique peptide motif, linear epitope, antigenicity, protein family, specificity
20	Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu 0001	An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes.	ISBRA	2007	DBLP DOI BibTeX RDF
20	Daniel A. S. Anjos, Gustavo G. Zerlotini, Guilherme A. Pinto, Maria Emília Telles Walter, Marcelo M. Brigido, Guilherme P. Telles, Carlos Juliano M. Viana, Nalvo F. Almeida	A Method for Inferring Biological Functions Using Homologous Genes Among Three Genomes.	BSB	2007	DBLP DOI BibTeX RDF
20	Changhui Yan, Jing Hu 0001	A Hidden Markov Model Approach to Identifying HTH Motifs Using Protein Sequence and Predicted Solvent Accessibility.	CIBCB	2006	DBLP DOI BibTeX RDF
20	Mehmet M. Dalkilic	An Architecture and Application for Integrating Curation Data at the Residue Level for Proteins.	DILS	2005	DBLP DOI BibTeX RDF
20	Haifeng Liu, Loo-Nin Teow	Performance Evaluation of Protein Sequence Clustering Tools.	International Conference on Computational Science (2)	2005	DBLP DOI BibTeX RDF
20	Umar Syed, Golan Yona	Using a mixture of probabilistic decision trees for direct prediction of protein function.	RECOMB	2003	DBLP DOI BibTeX RDF	functional prediction, sequence-function relationships, decision trees
20	Niranjan Nagarajan, Golan Yona	A multi-expert system for the automatic detection of protein domains from sequence information.	RECOMB	2003	DBLP DOI BibTeX RDF	domain boundaries, domain prediction, protein domains, SCOP
20	Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa S. Cline, Jill Cheng, Stephen A. Chervitz, David Kulp, Michael A. Siani-Rose	NetAffx: affymetrix probeset annotations.	SAC	2002	DBLP DOI BibTeX RDF	GRAPA, GeneChip, netaffx, microarray, protein domains