Literature DB >> 14696387

Simplicial neighborhood analysis of protein packing (SNAPP): a computational geometry approach to studying proteins.

Alexander Tropsha1, Charles W Carter, Stephen Cammer, Iosif I Vaisman.   

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Year:  2003        PMID: 14696387     DOI: 10.1016/S0076-6879(03)74022-1

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


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  13 in total

1.  Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.

Authors:  Stephen Cammer; Charles W Carter
Journal:  Bioinformatics       Date:  2010-02-03       Impact factor: 6.937

2.  An amino acid packing code for α-helical structure and protein design.

Authors:  Hyun Joo; Archana G Chavan; Jamie Phan; Ryan Day; Jerry Tsai
Journal:  J Mol Biol       Date:  2012-03-15       Impact factor: 5.469

3.  Discrimination of thermophilic and mesophilic proteins.

Authors:  Todd J Taylor; Iosif I Vaisman
Journal:  BMC Struct Biol       Date:  2010-05-17

4.  HIV-1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method.

Authors:  Shuxing Zhang; Andrew H Kaplan; Alexander Tropsha
Journal:  Proteins       Date:  2008-11-15

5.  ARID1a-DNA interactions are required for promoter occupancy by SWI/SNF.

Authors:  Ronald L Chandler; Jennifer Brennan; Jonathan C Schisler; Daniel Serber; Cam Patterson; Terry Magnuson
Journal:  Mol Cell Biol       Date:  2012-11-05       Impact factor: 4.272

6.  An Ancestral Tryptophanyl-tRNA Synthetase Precursor Achieves High Catalytic Rate Enhancement without Ordered Ground-State Tertiary Structures.

Authors:  Paul J Sapienza; Li Li; Tishan Williams; Andrew L Lee; Charles W Carter
Journal:  ACS Chem Biol       Date:  2016-04-07       Impact factor: 5.100

7.  Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

Authors:  Raed Khashan; Weifan Zheng; Alexander Tropsha
Journal:  Proteins       Date:  2012-06-07

8.  A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase.

Authors:  Maryna Kapustina; Violetta Weinreb; Li Li; Brian Kuhlman; Charles W Carter
Journal:  Structure       Date:  2007-10       Impact factor: 5.006

9.  Structural and functional analysis of multi-interface domains.

Authors:  Liang Zhao; Steven C H Hoi; Limsoon Wong; Tobias Hamp; Jinyan Li
Journal:  PLoS One       Date:  2012-12-14       Impact factor: 3.240

10.  Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys.

Authors:  Dan M Bolser; Ioannis Filippis; Henning Stehr; Jose Duarte; Michael Lappe
Journal:  BMC Struct Biol       Date:  2008-12-08
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