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FastContact: rapid estimate of contact and binding free energies

C. J. Camacho, C. Zhang
2005 Bioinformatics  
We report on the implementation of a fast computational estimate of the binding free energy based on a statistically determined desolvation contact potential and Coulomb electrostatics with a distance-dependent  ...  Although the problem of computing binding free energies remains open, approximate estimates have become very useful for filtering potential binding complexes.  ...  ACP and ACP-based binding energy function was developed by C. Zhang in collaboration with Drs. J. Cornette and G. Vasmatzis while working at Professor Charles DeLisi's laboratory.  ... 
doi:10.1093/bioinformatics/bti322 pmid:15713734 fatcat:aqeojltfmbfwpkhdwo5ctqug44

Classification of Protein Interactions Based on Sparse Discriminant Analysis and Energetic Features [chapter]

Katarzyna Stąpor, Piotr Fabian
2016 Lecture Notes in Computer Science  
These were computed using FastContact [4] , which obtains their fast estimates. FastContact delivers the electrostatic energy, solvation free energy, and the top 20 maximum and minimum values for:  ...  Protein-protein interaction classification method To characterize properties of protein interaction, we proposed to use the binding free energies.  ...  Rapid estimation of contact and binding free energies The estimation of contact and binding free energies may be in general a time consuming job.  ... 
doi:10.1007/978-3-319-45378-1_47 fatcat:57vmpdveqjfthfqtpegrf2bqla

Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity

Anand Krishnan V. Iyer, Kien T. Tran, Christopher W. Borysenko, Michael Cascio, Carlos J. Camacho, Harry C. Blair, Ivet Bahar, Alan Wells
2007 Journal of Cellular Physiology  
Normal mode analysis of both structures indicated that the binding pocket of EGFR exhibits a significantly higher mobility in Ten14-EGFR complex compared to that of the EGF-EGFR complex; we hypothesized  ...  In accordance with our predicted bound models, Ten14 in monomeric form does not bind EGFR with sufficient stability so as to induce degradation of receptor, or undergo EGFR-mediated internalization over  ...  Acknowledgments We thank Jonathan Steckbeck and the BIAcore facility at the University of Pittsburgh for help with using the machine. We thank Dr. Lee Wei Yang and other members of Dr.  ... 
doi:10.1002/jcp.20986 pmid:17311283 fatcat:kndbicavyff7vk2i23mrswvdsy

Selection of near-native poses in CAPRI rounds 13-19

Sanbo Qin, Huan-Xiang Zhou
2010 Proteins: Structure, Function, and Bioinformatics  
One scoring function used was FastContact, 16 which gives rapid estimates of contact and binding free energies.  ...  Part of the reason this model was promoted to the top was that the electrostatic free energy calculated by FastContact was very favorable.  ... 
doi:10.1002/prot.22772 pmid:20589642 pmcid:PMC2948629 fatcat:byu27cetnzcwvphpvbe4kvfkai

Probing protein flexibility reveals a mechanism for selective promiscuity

Nicolas A Pabon, Carlos J Camacho
2017 eLife  
Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly  ...  Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners.  ...  Acknowledgements This work was funded by the National Institute of Health (grant GM097082 to CJC) and the National Science Foundation (grant 1247842 to NAP).  ... 
doi:10.7554/elife.22889 pmid:28432789 pmcid:PMC5446241 fatcat:75dyhs7ydve2vgxrjg2u5pohgy

Recent Progress and Future Directions in Protein-Protein Docking

David Ritchie
2008 Current protein and peptide science  
, alanine scanning, and NMR residual dipolar coupling restraints to help identify key binding residues.  ...  These approaches can often produce a relatively small list of up to a few thousand orientations, amongst which a near-native binding mode is often observed.  ...  of the binding free energy of a complex.  ... 
doi:10.2174/138920308783565741 pmid:18336319 fatcat:yx4gggoo6bbsbg2vr2ifl7lnce

An affinity-enhanced, broadly neutralizing heavy chain-only antibody protects against SARS-CoV-2 infection in animal models

Bert Schepens, Loes van Schie, Wim Nerinckx, Kenny Roose, Wander Van Breedam, Daria Fijalkowska, Simon Devos, Wannes Weyts, Sieglinde De Cae, Sandrine Vanmarcke, Chiara Lonigro, Hannah Eeckhaut (+51 others)
2021 Science Translational Medicine  
Free energy contribution analysis by FastContact (20) of snapshots from Molecular Dynamics simulations with the VHH72-RBD complex indicates that the epitope recognized by VHH72 has a prominent two-residue  ...  After conversion of the trajectory to PDB-format, snapshots were extracted every 0.5 ns and were submitted to the FastContact 2.0 server (20) for binding energy calculations.  ... 
doi:10.1126/scitranslmed.abi7826 pmid:34609205 fatcat:z2z2m3wxufhaznqxobfx2koc6q

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
Protein-protein interface: a brief overview Proteins are usually involved in interactions with an estimated average of 5-10 protein partners [41] , the binding site(s) with these partners may or may not  ...  Different in silico methods have been developed to analyze the physical properties of proteins and learn more about how these properties are associated with binding.  ...  Acknowledgments Supports from the Inserm institute and Inserm-Transfert are greatly appreciated.  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

Drug development of an affinity enhanced, broadly neutralizing heavy chain only antibody that restricts SARS-CoV-2 in hamsters [article]

Bert Schepens, Loes van Schie, Wim Nerinckx, Kenny Roose, Wander Van Breedam, Daria Fijalkowska, Simon Devos, Wannes Weyts, Sieglinde De Cae, Sandrine Vanmarcke, Chiara Lonigro, Hannah Eeckhaut (+49 others)
2021 bioRxiv   pre-print
Additionally, we show that XVR011 is unaffected in its neutralizing capacity of currently rapidly spreading SARS-CoV-2 variants, and demonstrate its unique, wide scope of binding across the Sarbecovirus  ...  We have identified camelid single-domain antibodies (VHHs) that cross-neutralize SARS-CoV-1 and -2, such as VHH72, which binds to a unique highly conserved epitope in the viral receptor-binding domain  ...  Acknowledgements We thank Gert Zimmer, Stefan Pöhlmann and Markus Hoffmann for providing reagents to generate VSV pseudotype particles, Jason McLellan and Daniel Wrapp for providing SARS-CoV-2 spike and  ... 
doi:10.1101/2021.03.08.433449 fatcat:hx6w3ukgenggzgnhnksa7olyze

Epidermal Growth Factor Receptor [chapter]

Encyclopedic Reference of Cancer  
Activation of PLCγ and m-calpain, molecules associated with migration, were noted even at sub-saturating doses of Ten14.  ...  However, activation of ERK/MAPK, p90RSK and Elk1, factors affecting proliferation, remained low even at high Ten14 concentrations.  ...  We thank Jonathan Steckbeck and the BIAcore facility at the University of Pittsburgh for help with using the machine. We thank Dr. Lee Wei Yang and other members of Dr. Ivet Bahar's and Dr.  ... 
doi:10.1007/3-540-30683-8_515 fatcat:e63wwctmnvff7nyqttx2stiiuq

Epidermal Growth Factor Receptor [chapter]

Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine  
Activation of PLCγ and m-calpain, molecules associated with migration, were noted even at sub-saturating doses of Ten14.  ...  However, activation of ERK/MAPK, p90RSK and Elk1, factors affecting proliferation, remained low even at high Ten14 concentrations.  ...  We thank Jonathan Steckbeck and the BIAcore facility at the University of Pittsburgh for help with using the machine. We thank Dr. Lee Wei Yang and other members of Dr. Ivet Bahar's and Dr.  ... 
doi:10.1007/3-540-29623-9_6922 fatcat:zk64ntklxvbkvl5ewshxd4mtfy

Epidermal Growth Factor Receptor [chapter]

Encyclopedia of Cancer  
Activation of PLCγ and m-calpain, molecules associated with migration, were noted even at sub-saturating doses of Ten14.  ...  However, activation of ERK/MAPK, p90RSK and Elk1, factors affecting proliferation, remained low even at high Ten14 concentrations.  ...  We thank Jonathan Steckbeck and the BIAcore facility at the University of Pittsburgh for help with using the machine. We thank Dr. Lee Wei Yang and other members of Dr. Ivet Bahar's and Dr.  ... 
doi:10.1007/978-3-540-47648-1_1932 fatcat:4br756o6kvhubmghivpdx6sege