Ravi Radhakrishnan, Karunesh Arora, Yanli Wang, William A. Beard, Samuel H. Wilson, Tamar Schlick
Structural [1], kinetic [2], and computational data [3] have suggested that the large subdomain movement per se in the polymerase cycle is relatively rapid, while Arg258 side-chain rotation could be...
Direct imaging of titania nanotubes located in mouse neural stem cell nuclei (2009)
Wang, Yanli, Wang, Jia, Deng, Xiaoyong, Wang, Jiao, Wang, Haifang, Wu, Minghong, ...
Titania nanotubes (TiO2-NTs) are a potential drug vehicle for use in nanomedicine. To this end, a preliminary study of the interaction of a model cell with TiO2-NTs has been carried out. TiO2-NTs...
Thompson, Kenneth, Wang, Yanli, Madej, Tom, Bryant, Stephen H
Abstract Background The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search...
PubChem: a public information system for analyzing bioactivities of small molecules (2009)
Wang, Yanli, Xiao, Jewen, Suzek, Tugba O., Zhang, Jian, Wang, Jiyao, Bryant, Stephen H.
PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently...
A survey of across-target bioactivity results of small molecules in PubChem (2009)
Han, Lianyi, Wang, Yanli, Bryant, Stephen H.
This work provides an analysis of across-target bioactivity results in the screening data deposited in PubChem. Two alternative approaches for grouping-related targets are used to examine a...
Han, Lianyi, Wang, Yanli, Bryant, Stephen H
Abstract Background Recent advances in high-throughput screening (HTS) techniques and readily available compound libraries generated using combinatorial chemistry or derived from natural products...
Dietary quality 1 year after diagnosis of coronary heart disease (2008)
Ma, Yunsheng, Li, Wenjun, Olendzki, Barbara C., Pagoto, Sherry L., Merriam, Philip A., Chiriboga, David E., ...
OBJECTIVE: The purpose of this ancillary study is to determine the quality of diets in patients with documented coronary heart disease (CHD). DESIGN: Dietary data were originally collected using a...
Abstract Background 8-Oxoguanine (8-oxo G ) is a common oxidative lesion frequently encountered by DNA polymerases such as the repair enzyme DNA polymerase β (pol β). To interpret in atomic and...
Jungnickel, Melissa K., Sutton, Keith A., Wang, Yanli, Florman, Harvey M.
Sperm of many animals must complete an exocytotic event, the acrosome reaction, in order to fuse with eggs. In mammals, acrosome reactions are triggered during sperm contact with the egg...
MMDB: annotating protein sequences with Entrez's 3D-structure database (2007)
Wang, Yanli, Addess, Kenneth J., Chen, Jie, Geer, Lewis Y., He, Jane, He, Siqian, ...
Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a...
BMC Structural Biology BioMed Central (2007)
Yanli Wang, Tamar Schlick, Yanli Wang, Tamar Schlick
Research article Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides
Wang, Yanli, Arora, Karunesh, Schlick, Tamar
The possible conformational changes of DNA polymerase IV (Dpo4) before and after the nucleotidyl-transfer reaction are investigated at the atomic level by dynamics simulations to gain insight into...
Tang, Shengjian, Wang, Xiaoke, Lin, Lixin, Sun, Yan, Wang, Yanli, Yu, Hongbo
Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is an autosomal dominant disorder characterized by blepharophimosis, ptosis and epicanthus inversus. Based on the presence and absence of...
Yanli Wang, Sujatha Reddy, William A. Beard, Tamar Schlick
ABSTRACT To elucidate how human DNA polymerase b (pol b) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical...
Ravi Radhakrishnan, Karunesh Arora, Yanli Wang, William A. Beard, Samuel H. Wilson, Tamar Schlick
ABSTRACT: With an increasing number of structural, kinetic, and modeling studies of diverse DNA polymerases in various contexts, a complex dynamical view of how atomic motions might define molecular...
Yanli Wang, Karunesh Arora, Tamar Schlick, Email Alerting, Yanli Wang, Karunesh Arora, ...
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass
The Effect of Dividend Initiations on Stock Returns: A Propensity Score Matching Approach (2005)
This paper measures the effect of dividend initiation announcements on firms ’ stock returns using a propensity score matching approach. Unlike the traditional event study methodology, propensity...
CDD: a curated Entrez database of conserved domain alignments (2003)
Marchler-Bauer, Aron, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE®. This allows users to search for domain types...
MMDB: Entrez's 3D-structure database (2003)
Chen, Jie, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's...
DOI: 10.1093/nar/gkg086 MMDB: Entrez’s 3D-structure database (2002)
Jie Chen, John B. Anderson, Carol Deweese-scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, ...
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of...
MMDB: Entrez's 3D-structure database (2002)
Wang, Yanli, Anderson, John B., Chen, Jie, Geer, Lewis Y., He, Siqian, Hurwitz, David I., ...
Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of...
MMDB: 3D structure data in Entrez (2000)
Wang, Yanli, Addess, Kenneth J., Geer, Lewis, Madej, Thomas, Marchler-Bauer, Aron, Zimmerman, Diane, ...
Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure...
Links from Genome Proteins to Known 3-D Structures (2000)
Wang, Yanli, Bryant, Stephen, Tatusov, Roman, Tatusova, Tatiana
Position-dependent protein mutant profile based on mean force field calculation. Protein Eng (1996)
Yanli Wang, Luhua Lai, Shuwei Li, Yuzhaen Han, Youqi Tang
calculation
Typescript.
MMDB: Entrez’s 3D-structure database
Wang, Yanli, Anderson, John B., Chen, Jie, Geer, Lewis Y., He, Siqian, Hurwitz, David I., ...
Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of...
MMDB: 3D structure data in Entrez
Wang, Yanli, Addess, Kenneth J., Geer, Lewis, Madej, Thomas, Marchler-Bauer, Aron, Zimmerman, Diane, ...
Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure...
MMDB: Entrez's 3D-structure database
Chen, Jie, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's...
CDD: a curated Entrez database of conserved domain alignments
Marchler-Bauer, Aron, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE®. This allows users to search for domain types...
Links from Genome Proteins to Known 3-D Structures
Wang, Yanli, Bryant, Stephen, Tatusov, Roman, Tatusova, Tatiana
We describe a genome annotation service provided by the Entrez browser, http://www.ncbi.nlm.nih.gov/entrez. All protein products identified in fully sequenced microbial genomes have been compared...
Insight into the Structural Role of Carotenoids in the Photosystem I: A Quantum Chemical Analysis
Wang, Yanli, Mao, Lisong, Hu, Xiche
The structural stabilization role of carotenoids in the formation of photosynthetic pigment-protein complexes is investigated theoretically. The π–π stacking and CH-π interactions between...
MMDB: Entrez’s 3D-structure database
Wang, Yanli, Anderson, John B., Chen, Jie, Geer, Lewis Y., He, Siqian, Hurwitz, David I., ...
Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of...
MMDB: 3D structure data in Entrez
Wang, Yanli, Addess, Kenneth J., Geer, Lewis, Madej, Thomas, Marchler-Bauer, Aron, Zimmerman, Diane, ...
Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure...
MMDB: Entrez's 3D-structure database
Chen, Jie, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's...
CDD: a curated Entrez database of conserved domain alignments
Marchler-Bauer, Aron, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, ...
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE®. This allows users to search for domain types...
Links from Genome Proteins to Known 3-D Structures
Wang, Yanli, Bryant, Stephen, Tatusov, Roman, Tatusova, Tatiana
We describe a genome annotation service provided by the Entrez browser, http://www.ncbi.nlm.nih.gov/entrez. All protein products identified in fully sequenced microbial genomes have been compared...
Insight into the Structural Role of Carotenoids in the Photosystem I: A Quantum Chemical Analysis
Wang, Yanli, Mao, Lisong, Hu, Xiche
The structural stabilization role of carotenoids in the formation of photosynthetic pigment-protein complexes is investigated theoretically. The π–π stacking and CH-π interactions between...
MMDB: annotating protein sequences with Entrez's 3D-structure database
Wang, Yanli, Addess, Kenneth J., Chen, Jie, Geer, Lewis Y., He, Jane, He, Siqian, ...
Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a...
Wang, Yanli, Arora, Karunesh, Schlick, Tamar
The possible conformational changes of DNA polymerase IV (Dpo4) before and after the nucleotidyl-transfer reaction are investigated at the atomic level by dynamics simulations to gain insight into...
Wang, Yanli, Reddy, Sujatha, Beard, William A., Wilson, Samuel H., Schlick, Tamar
To elucidate how human DNA polymerase β (pol β) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step...
Li, Xu, Huang, Hua, Song, Xiaomin, Wang, Yanli, Xu, Hang, Teng, Maikun, ...
Preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from L. interrogans.
PubChem: a public information system for analyzing bioactivities of small molecules
Wang, Yanli, Xiao, Jewen, Suzek, Tugba O., Zhang, Jian, Wang, Jiyao, Bryant, Stephen H.
PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently...
A survey of across-target bioactivity results of small molecules in PubChem
Han, Lianyi, Wang, Yanli, Bryant, Stephen H.
This work provides an analysis of across-target bioactivity results in the screening data deposited in PubChem. Two alternative approaches for grouping-related targets are used to examine a...