AS2TS system for protein structure modeling and analysis

Keywords

Protein Data Bank (RCSB PDB), Protein Data Bank, Protein structure database, Homology modeling, Protein structure

References

• Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.Michael J. Bower, Fred E. Cohen, Roland L. Dunbrack — 1997
• Identification of common molecular subsequences.Temple F. Smith, Michael S. Waterman — 1981
• Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.William R. Pearson — 1991
• LGA: a method for finding 3D similarities in protein structuresAdam Zemła — 2003
• Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway.Katherine A. Kantardjieff, Chang‐Yub Kim, Cleo M. Naranjo — 2004
• Assessment of progress over the CASP experiments??eslovas Venclovas, Adam Zemła, Krzysztof Fidelis — 2003
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Stephen F. Altschul — 1997
• Bovine enterovirus 2: complete genomic sequence and molecular modelling of a reference strain and a wild-type isolate from endemically infected US cattle.S. Denise Goens, Sebastian Botero, Adam Zemła — 2004
• Critical assessment of methods of protein structure prediction (CASP)—Round 6John Moult, Krzysztof Fidelis, Burkhard Rost — 2005
• Bovine Enterovirus Type 2. Complete Genomic Sequence and Molecular Modeling of a Reference Strain and a Wild Type Isolate from Endemically Infected US Cattle.Cai-Quan Zhou, Adam Zemła, S. Denise Goens — 2004
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data BankH. Berman, Tammy Battistuz, T. N. Bhat

Cited by

• Two processivity clamp interactions differentially alter the dual activities of UmuC伸夫 三橋, 信義 藤本, 祐基 西城 — 2006
• Computational Identification of Protein Catalytic Sites: Tests, ValidationDaniel Kirshner, Jerome P. Nilmeier, Felice C. Lightstone — 2011
• Identification of drug leads against HCV and malaria using different target proteinsR. A. Olaby — 2014
• A Non-cleavable UmuD Variant That Acts as a UmuD′ Mimic*Penny J. Beuning, Sharotka M. Simon, Adam Zemła — 2006
• Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysisEliza Wiech, Hai‐Ping Cheng, Shaneen Singh — 2015
• Endothelial cells anchoring by functionalized yeast polypeptide.Jie Xu, Xiaolin Zhou, Haiyan Ge — 2008
• The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host EnvironmentsMonica K. Borucki, Jonathan Allen, Haiyin Chen‐Harris — 2013
• Promiscuity, stability and cold adaptation of a newly isolated acylaminoacyl peptidase.Electra Brunialti, Pietro Gatti‐Lafranconi, Marina Lotti — 2011
• Structural Basis for the Recognition of Human Cytomegalovirus Glycoprotein B by a Neutralizing Human AntibodyNadja Spindler, Uschi Diestel, Joachim D. Stump — 2014
• Crystal Structure of the HIV-2 Neutralizing Fab Fragment 7C8 with High Specificity to the V3 Region of gp125Hannes Uchtenhagen, Rosmarie Friemann, Grzegorz Raszewski — 2011
• Amino acid and structural variability of Yersinia pestis LcrV proteinAndrey P. Anisimov, Svetlana V. Dentovskaya, E. A. Panfertsev — 2009
• SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation StudiesAnu Chakicherla, Carol Zhou, Martha Ligon Dang — 2009
• Integrating Ion Mobility Mass Spectrometry with Molecular Modelling to Determine the Architecture of Multiprotein ComplexesArgyris Politis, Ah Young Park, Suk‐Joon Hyung — 2010
• A role for loop F in modulating GABA binding affinity in the GABA(A) receptor.Timothy S. Carpenter, Edmond Y. Lau, Felice C. Lightstone — 2012
• Automatic procedure for using models of proteins in molecular replacementDomenico Raimondo, Alejandro Giorgetti, Alejandro Giorgetti — 2006
• Year 2 Report: Protein Function Prediction PlatformUSDOE, Carol Zhou, Defense Threat Reduction Agency (DTRA) — 2012
• Opening of the Outer Membrane Protein Channel in Tripartite Efflux Pumps Is Induced by Interaction with the Membrane Fusion PartnerThamarai K. Janganan, Li Zhang, Vassiliy N. Bavro — 2010
• Identification of a Novel Drug Lead That Inhibits HCV Infection and Cell-to-Cell Transmission by Targeting the HCV E2 GlycoproteinReem R. Al Olaby, Laurence Cocquerel, Adam Zemła — 2014
• TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling.Sebastian Trojanowski, Aleksandra Rutkowska, Andrzej Koliński — 2010
• Computational approaches for identification of conserved/unique binding pockets in the A chain of ricinC. Zhou, Adam Zemła, D. Christopher Roe — 2005

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