Results 61 to 70 of about 760,069 (270)

Knowledge-based energy functions for computational studies of proteins

, 2006
This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design.
A. Ben-Naim, A. Godzik, A. Godzik, A. Rossi, A.J. Bordner, A.V. Finkelstein, B. Fain, B. Krishnamoorthy, B. Kuhlman, B. Schölkopf, B.H. Park, B.I. Dahiyat, B.J. McConkey, B.O. Mitchell, C. Anfinsen, C. Carter Jr., C. Czaplewski, C. Hoppe, C. Hu, C. Micheletti, C. Papadimitriou, C. Zhang, C. Zhang, C. Zhang, C. Zhang, C. Zhang, C.A. Rohl, C.B. Anfinsen, C.M.R Lemer, C.S. Mészáros, D. Gilis, D. Gilis, D. Gilis, D. Tobi, D. Xu, E. Venclovas, E.I. Shakhnovich, E.I. Shakhnovich, F.A. Momany, H. Dobbs, H. Edelsbrunner, H. Gan, H. Li, H. Li, H. Lu, H. Zhou, H.S. Chan, I. Muegge, J. Khatun, J. Liang, J.A. Kocher, J.A. Rank, J.M. Deutsch, J.R. Bienkowska, K. Nishikawa, K. Sale, K.H. Lee, K.K. Koretke, K.K. Koretke, K.T. Simons, L. Adamian, L. Adamian, L. Adamian, L.A. Mirny, L.L. Looger, L.M. Amzel, M. Karplus, M. Levitt, M. Vendruscolo, M. Vendruscolo, M.H. Hao, M.H. Hao, M.J. Sippl, M.J. Sippl, M.J. Sippl, M.P. Eastwood, M.R. Betancourt, M.S. Friedrichs, N. Karmarkar, N.V. Buchete, N.V. Buchete, P. Koehl, P. Koehl, P.D. Thomas, P.D. Thomas, P.G. Wolynes, P.J. Munson, R. Goldstein, R. Guerois, R. Jackups Jr., R. Janicke, R. Méndez, R. Samudrala, R. Samudrala, R.B. Hill, R.I. Dima, R.J. Vanderbei, R.K. Singh, R.L. Jernigan, R.S. DeWitte, S. Liu, S. Miyazawa, S. Miyazawa, S. Miyazawa, S. Shimizu, S. Shimizu, S. Tanaka, S.J. Wodak, T. Kortemme, T. Kortemme, T. Kortemme, T. Lazaridis, T.L. Chiu, U. Bastolla, U. Bastolla, V. Vapnik, V. Vapnik, V.N. Maiorov, W.P. Russ, X. Li, X. Li, Y. Duan, Y. Park, Y. Xia   +123 more
core   +1 more source

The planar cell polarity protein Vangl2 interacts with the PDZ‐domains of Scribble but not with a unique PDZ‐like domain in Inturned

FEBS Letters, EarlyView.
Structural and biochemical characterisations show that the planar cell polarity (PCP) protein Inturned harbours a unique PDZ‐like domain that does not bind canonical PDZ‐binding motifs (PBMs) like that of another PCP protein Vangl2. In contrast, the apical‐basal polarity protein Scribble contains four PDZ domains that bind Vangl2, but one PDZ domain ...
Stephan Wilmes, Jan Brysch, Carmen Gelze, Lilli Meier, Daniel Kümmel   +4 more
wiley   +1 more source

PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold

eLife
Protein-protein interactions underlie nearly all cellular processes. With the advent of protein structure prediction methods such as AlphaFold2 (AF2), models of specific protein pairs can be built extremely accurately in most cases.
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas   +3 more
doaj   +1 more source

Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

BMC Bioinformatics, 2021
Background Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure.
Siyuan Liu, Tong Wang, Qijiang Xu, Bin Shao, Jian Yin, Tie-Yan Liu   +5 more
doaj   +1 more source

Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31 [PDF]

, 2012
The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families.
E Nakkeeran, N S. Sardeshmukh, S G. Sanmukh   +2 more
core   +1 more source

Recoverable One-dimensional Encoding of Three-dimensional Protein Structures

, 2005
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence.
A. R. Kinjo, Berman, Havel, K. Nishikawa, Kabsch, Kinjo, Nakai, Plaxco, Porto, Vendruscolo, Wang   +10 more
core   +2 more sources

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Predicting diverse M-best protein contact maps

, 2015
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging.
Ma, Jianzhu, Sun, Siqi, Wang, Sheng, Xu, Jinbo   +3 more
core   +1 more source

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

FEBS Letters, EarlyView.
A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa, Konstantinos Makryniotis, Theofani‐Iosifina Sousani, Evangelos Topakas, Vangelis Daskalakis, Maria Dimarogona   +5 more
wiley   +1 more source

Bayesian models and algorithms for protein beta-sheet prediction [PDF]

, 2009
Prediction of the three-dimensional structure greatly benefits from the information related to secondary structure, solvent accessibility, and non-local contacts that stabilize a protein's structure.
Altunbasak, Yucel, Altunbaşak, Yücel, Aydın, Zafer, Aydin, Zafer, Erdogan, Hakan, Erdoğan, Hakan   +5 more
core