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Literature DB >> 19429600

FlexServ: an integrated tool for the analysis of protein flexibility.

Jordi Camps¹, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluís Gelpí, Modesto Orozco.

Abstract

SUMMARY: FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics. AVAILABILITY: http://mmb.pcb.ub.es/FlexServ; http://www.inab.org

Entities: Disease

Mesh：

Substances：
Proteins

Year: 2009 PMID： 19429600 DOI： 10.1093/bioinformatics/btp304

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

29 in total

1. Modification of interface between regulatory and essential light chains hampers phosphorylation-dependent activation of smooth muscle myosin.

Authors: Shaowei Ni; Feng Hong; Brian D Haldeman; Josh E Baker; Kevin C Facemyer; Christine R Cremo
Journal: J Biol Chem Date: 2012-05-01 Impact factor: 5.157

2. Comparative homology modeling of pyruvate dehydrogenase kinase isozymes from Xenopus tropicalis reveals structural basis for their subfunctionalization.

Authors: Alexander A Tokmakov
Journal: J Mol Model Date: 2011-11-09 Impact factor: 1.810

3. Expression profiling and in silico homology modeling of Inositol pentakisphosphate 2-kinase, a potential candidate gene for low phytate trait in soybean.

Authors: Nabaneeta Basak; Veda Krishnan; Vanita Pandey; Mansi Punjabi; Alkesh Hada; Ashish Marathe; Monica Jolly; Bhagath Kumar Palaka; Dinakara R Ampasala; Archana Sachdev
Journal: 3 Biotech Date: 2020-05-27 Impact factor: 2.406

4. Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function.

Authors: G Aaron Hobbs; Harsha P Gunawardena; Rachael Baker; Sharon L Campbell
Journal: Small GTPases Date: 2013-09-12

Review 5. Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.

Authors: Lidio Meireles; Mert Gur; Ahmet Bakan; Ivet Bahar
Journal: Protein Sci Date: 2011-09-09 Impact factor: 6.725

FlexServ: an integrated tool for the analysis of protein flexibility.

1. Modification of interface between regulatory and essential light chains hampers phosphorylation-dependent activation of smooth muscle myosin.

2. Comparative homology modeling of pyruvate dehydrogenase kinase isozymes from Xenopus tropicalis reveals structural basis for their subfunctionalization.

3. Expression profiling and in silico homology modeling of Inositol pentakisphosphate 2-kinase, a potential candidate gene for low phytate trait in soybean.

4. Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function.

Review 5. Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.

6. Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding?

7. iMODS: internal coordinates normal mode analysis server.

8. ProDy: protein dynamics inferred from theory and experiments.

9. NAFlex: a web server for the study of nucleic acid flexibility.

10. ΔΔPT: a comprehensive toolbox for the analysis of protein motion.