Prediction of enzyme function by combining sequence similarity and protein interactions (2008)
Espadaler, Jordi, Eswar, Narayanan, Querol, Enrique, Avilés, Francesc X, Sali, Andrej, Marti-Renom, Marc A, ...
Abstract Background A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the...
Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios (2008)
Rachel Karchin, Mukesh Agarwal, Andrej Sali, Fergus Couch, Mary S. Beattie
Background: Missense (amino-acid changing) variants found in cancer predisposition genes often create difficulties when clinically interpreting genetic testing results. Although bioinformatics has...
Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios (2008)
Rachel Karchin, Mukesh Agarwal, Andrej Sali, Fergus Couch, Mary S. Beattie
Background: Missense (amino-acid changing) variants found in cancer predisposition genes often create difficulties when clinically interpreting genetic testing results. Although bioinformatics has...
Kanika Bajaj, M. S. Madhusudhan, Bharat V. Adkar, Purbani Chakrabarti, C. Ramakrishnan, Andrej Sali, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The ϕ dihedral angle of Pro is constrained to...
Bajaj, Kanika, Madhusudhan, MS, Adkar, Bharat V, Chakrabarti, Purbani, Ramakrishnan, C, Sali, Andrej, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The \phi dihedral angle of Pro is constrained to...
Kanika Bajaj, M.S. Madhusudhan, Bharat V Adkar, Purbani Chakrabarti, C Ramakrishnan, Andrej Sali, ...
When incorporated into a polypeptide chain, Proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The φ dihedral angle of Pro is constrained to...
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions (2007)
Ramon Aragues, Andrej Sali, Jaume Bonet, Baldo Oliva
The characterization of protein interactions is essential for understanding biological systems. While genome-scale methods are available for identifying interacting proteins, they do not pinpoint the...
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions (2007)
Ramon Aragues, Andrej Sali, Jaume Bonet, Marc Marti-Renom, Baldomero Oliva
The characterization of protein interactions is essential for understanding biological systems. While genome-scale methods are available for identifying interacting proteins, they do not pinpoint the...
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures (2007)
Marti-Renom, Marc A, Rossi, Andrea, Al-Shahrour, Fátima, Davis, Fred P, Pieper, Ursula, Dopazo, Joaquín, ...
Abstract Background Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half...
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning (2007)
Rachel Karchin, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
Many individuals tested for inherited cancer susceptibility at the BRCA1 gene locus are discovered to have variants of unknown clinical significance (UCVs). Most UCVs cause a single amino acid...
Bajaj, Kanika, Madhusudhan, MS, Adkar, Bharat V, Chakrabarti, Purbani, Ramakrishnan, C, Sali, Andrej, ...
When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The \phi dihedral angle of Pro is constrained to...
Functional impact of missense variants in BRCA1 predicted by supervised learning (2006)
Rachel Karchin, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej Sali
Many individuals tested for inherited cancer susceptibility at the BRCA1 gene locus are discovered to have variants of unknown clinical significance (UCVs) . Most UCVs cause a single amino acid...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 (2006)
Korkin, Dmitry, Davis, Fred P., Alber, Frank, Luong, Tinh, Shen, Min-Yi, Lucic, Vladan, ...
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 (2006)
Korkin, Dmitry, Davis, Fred P., Alber, Frank, Luong, Tinh, Shen, Min-Yi, Lucic, Vladan, ...
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 (2006)
Dmitry Korkin, Fred P. Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, ...
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 (2006)
Dmitry Korkin, Fred P. Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, ...
We describe comparative patch analysis for modeling the structures of multi-domain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...
Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T. Chait, Andrej Sali, ...
Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T. Chait, Andrej Sali, ...
Finding Cures for Tropical Diseases: Is Open Source an Answer? (2004)
Rai, Arti K., Maurer, Stephen M., Sali, Andrej
abstract not available
Finding Cures for Tropical Diseases: Is Open Source an Answer? (2004)
Rai, Arti K., Maurer, Stephen M., Sali, Andrej
abstract not available
Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T. Chait, Andrej Sali, ...
Structural similarities between the proteins of a nuclear pore subcomplex and proteins comprising vesicle coating complexes indicate a common origin for nuclear pore complexes and coated vesicles.
Finding Cures for Tropical Diseases: Is Open Source an Answer? (2004)
Stephen M. Maurer, Arti Rai, Andrej Sali
The Tropical Disease Initiative will be a Web-based, community- wide effort where scientists from the public and private sectors join together to discover new treatments.
Finding Cures for Tropical Diseases: Is Open Source an Answer? (2004)
Rai, Arti K., Maurer, Stephen M., Sali, Andrej
abstract not available
Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T. Chait, Andrej Sali, ...
Numerous features distinguish prokaryotes from eukaryotes, chief among which are the distinctive internal membrane systems of eukaryotic cells. These membrane systems form elaborate compartments and...
EVA: continuous automatic evaluation of protein structure prediction servers (2001)
Volker A. Eyrich, Dariusz Przybylski, Mallur S, Andrs Fiser, Florencio Pazos, ...
153 words; Text 1129 words; 5 References Abstract Summary: Evaluation of protein structure prediction methods is difficult and timeconsuming. Here, we describe EVA, a web server for assessing protein...
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
Identification and characterization of a p53 homologue in Drosophila melanogaster
Jin, Shengkan, Martinek, Sebastian, Joo, Woo S., Wortman, Jennifer R., Mirkovic, Nebojsa, Sali, Andrej, ...
The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety...
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
Sánchez, Roberto, Sali, Andrej
The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging...
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis
Bonanno, Jeffrey B., Edo, Carme, Eswar, Narayanan, Pieper, Ursula, Romanowski, Michael J., Ilyin, Valentin, ...
X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a...
MODBASE, a database of annotated comparative protein structure models
Pieper, Ursula, Eswar, Narayanan, Stuart, Ashley C., Ilyin, Valentin A., Sali, Andrej
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein...
Comparative protein structure modeling by iterative alignment, model building and model assessment
Comparative or homology protein structure modeling is severely limited by errors in the alignment of a modeled sequence with related proteins of known three-dimensional structure. To ameliorate this...
Tools for comparative protein structure modeling and analysis
Eswar, Narayanan, John, Bino, Mirkovic, Nebojsa, Fiser, Andras, Ilyin, Valentin A., Pieper, Ursula, ...
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints;...
EVA: evaluation of protein structure prediction servers
Koh, Ingrid Y. Y., Eyrich, Volker A., Marti-Renom, Marc A., Przybylski, Dariusz, Madhusudhan, Mallur S., Eswar, Narayanan, ...
EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope...
MODBASE, a database of annotated comparative protein structure models, and associated resources
Pieper, Ursula, Eswar, Narayanan, Braberg, Hannes, Madhusudhan, M. S., Davis, Fred P., Stuart, Ashley C., ...
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure....
Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture
Devos, Damien, Dokudovskaya, Svetlana, Alber, Frank, Williams, Rosemary, Chait, Brian T, Sali, Andrej, ...
Numerous features distinguish prokaryotes from eukaryotes, chief among which are the distinctive internal membrane systems of eukaryotic cells. These membrane systems form elaborate compartments and...
High-Throughput Computational and Experimental Techniques in Structural Genomics
Chance, Mark R., Fiser, Andras, Sali, Andrej, Pieper, Ursula, Eswar, Narayanan, Xu, Guiping, ...
Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome...
Finding Cures for Tropical Diseases: Is Open Source an Answer?
Maurer, Stephen M, Rai, Arti, Sali, Andrej
The Tropical Disease Initiative will be a Web-based, community- wide effort where scientists from the public and private sectors join together to discover new treatments
Devos, Damien, Dokudovskaya, Svetlana, Alber, Frank, Williams, Rosemary, Chait, Brian T, Sali, Andrej, ...
Detecting remotely related proteins by their interactions and sequence similarity
Espadaler, Jordi, Aragüés, Ramón, Eswar, Narayanan, Marti-Renom, Marc A., Querol, Enrique, Avilés, Francesc X., ...
The function of an uncharacterized protein is usually inferred either from its homology to, or its interactions with, characterized proteins. Here, we use both sequence similarity and protein...
MODBASE: a database of annotated comparative protein structure models and associated resources
Pieper, Ursula, Eswar, Narayanan, Davis, Fred P., Braberg, Hannes, Madhusudhan, M. S., Rossi, Andrea, ...
MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated...
Protein complex compositions predicted by structural similarity
Davis, Fred P., Braberg, Hannes, Shen, Min-Yi, Pieper, Ursula, Sali, Andrej, Madhusudhan, M.S.
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we...
Simple fold composition and modular architecture of the nuclear pore complex
Devos, Damien, Dokudovskaya, Svetlana, Williams, Rosemary, Alber, Frank, Eswar, Narayanan, Chait, Brian T., ...
The nuclear pore complex (NPC) consists of multiple copies of ≈30 different proteins [nucleoporins (nups)], forming a channel in the nuclear envelope that mediates macromolecular transport between...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Korkin, Dmitry, Davis, Fred P, Alber, Frank, Luong, Tinh, Shen, Min-Yi, Lucic, Vladan, ...
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...
Identification and characterization of a p53 homologue in Drosophila melanogaster
Jin, Shengkan, Martinek, Sebastian, Joo, Woo S., Wortman, Jennifer R., Mirkovic, Nebojsa, Sali, Andrej, ...
The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety...
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
Sánchez, Roberto, Sali, Andrej
The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging...
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis
Bonanno, Jeffrey B., Edo, Carme, Eswar, Narayanan, Pieper, Ursula, Romanowski, Michael J., Ilyin, Valentin, ...
X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a...
MODBASE, a database of annotated comparative protein structure models
Pieper, Ursula, Eswar, Narayanan, Stuart, Ashley C., Ilyin, Valentin A., Sali, Andrej
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein...
Comparative protein structure modeling by iterative alignment, model building and model assessment
Comparative or homology protein structure modeling is severely limited by errors in the alignment of a modeled sequence with related proteins of known three-dimensional structure. To ameliorate this...
Tools for comparative protein structure modeling and analysis
Eswar, Narayanan, John, Bino, Mirkovic, Nebojsa, Fiser, Andras, Ilyin, Valentin A., Pieper, Ursula, ...
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints;...
EVA: evaluation of protein structure prediction servers
Koh, Ingrid Y. Y., Eyrich, Volker A., Marti-Renom, Marc A., Przybylski, Dariusz, Madhusudhan, Mallur S., Eswar, Narayanan, ...
EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope...
MODBASE, a database of annotated comparative protein structure models, and associated resources
Pieper, Ursula, Eswar, Narayanan, Braberg, Hannes, Madhusudhan, M. S., Davis, Fred P., Stuart, Ashley C., ...
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure....
Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture
Devos, Damien, Dokudovskaya, Svetlana, Alber, Frank, Williams, Rosemary, Chait, Brian T, Sali, Andrej, ...
Numerous features distinguish prokaryotes from eukaryotes, chief among which are the distinctive internal membrane systems of eukaryotic cells. These membrane systems form elaborate compartments and...
High-Throughput Computational and Experimental Techniques in Structural Genomics
Chance, Mark R., Fiser, Andras, Sali, Andrej, Pieper, Ursula, Eswar, Narayanan, Xu, Guiping, ...
Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome...
Finding Cures for Tropical Diseases: Is Open Source an Answer?
Maurer, Stephen M, Rai, Arti, Sali, Andrej
The Tropical Disease Initiative will be a Web-based, community- wide effort where scientists from the public and private sectors join together to discover new treatments
Devos, Damien, Dokudovskaya, Svetlana, Alber, Frank, Williams, Rosemary, Chait, Brian T, Sali, Andrej, ...
Detecting remotely related proteins by their interactions and sequence similarity
Espadaler, Jordi, Aragüés, Ramón, Eswar, Narayanan, Marti-Renom, Marc A., Querol, Enrique, Avilés, Francesc X., ...
The function of an uncharacterized protein is usually inferred either from its homology to, or its interactions with, characterized proteins. Here, we use both sequence similarity and protein...
MODBASE: a database of annotated comparative protein structure models and associated resources
Pieper, Ursula, Eswar, Narayanan, Davis, Fred P., Braberg, Hannes, Madhusudhan, M. S., Rossi, Andrea, ...
MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated...
Simple fold composition and modular architecture of the nuclear pore complex
Devos, Damien, Dokudovskaya, Svetlana, Williams, Rosemary, Alber, Frank, Eswar, Narayanan, Chait, Brian T., ...
The nuclear pore complex (NPC) consists of multiple copies of ≈30 different proteins [nucleoporins (nups)], forming a channel in the nuclear envelope that mediates macromolecular transport between...
Protein complex compositions predicted by structural similarity
Davis, Fred P., Braberg, Hannes, Shen, Min-Yi, Pieper, Ursula, Sali, Andrej, Madhusudhan, M.S.
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we...
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Korkin, Dmitry, Davis, Fred P, Alber, Frank, Luong, Tinh, Shen, Min-Yi, Lucic, Vladan, ...
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of...